Aureimonas Leprariae Sp. Nov., Isolated from a Lepraria Sp. Lichen
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The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. -
Ice-Nucleating Particles Impact the Severity of Precipitations in West Texas
Ice-nucleating particles impact the severity of precipitations in West Texas Hemanth S. K. Vepuri1,*, Cheyanne A. Rodriguez1, Dimitri G. Georgakopoulos4, Dustin Hume2, James Webb2, Greg D. Mayer3, and Naruki Hiranuma1,* 5 1Department of Life, Earth and Environmental Sciences, West Texas A&M University, Canyon, TX, USA 2Office of Information Technology, West Texas A&M University, Canyon, TX, USA 3Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA 4Department of Crop Science, Agricultural University of Athens, Athens, Greece 10 *Corresponding authors: [email protected] and [email protected] Supplemental Information 15 S1. Precipitation and Particulate Matter Properties S1.1 Precipitation Categorization In this study, we have segregated our precipitation samples into four different categories, such as (1) snows, (2) hails/thunderstorms, (3) long-lasted rains, and (4) weak rains. For this categorization, we have considered both our observation-based as well as the disdrometer-assigned National Weather Service (NWS) 20 code. Initially, the precipitation samples had been assigned one of the four categories based on our manual observation. In the next step, we have used each NWS code and its occurrence in each precipitation sample to finalize the precipitation category. During this step, a precipitation sample was categorized into snow, only when we identified a snow type NWS code (Snow: S-, S, S+ and/or Snow Grains: SG). Likewise, a precipitation sample was categorized into hail/thunderstorm, only when the cumulative sum of NWS codes for hail was 25 counted more than five times (i.e., A + SP ≥ 5; where A and SP are the codes for soft hail and hail, respectively). -
Microbial Community Composition During Degradation of Organic Matter
TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl für Bodenökologie Microbial community composition during degradation of organic matter Stefanie Elisabeth Wallisch Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. A. Göttlein Prüfer der Dissertation: 1. Hon.-Prof. Dr. M. Schloter 2. Univ.-Prof. Dr. S. Scherer Die Dissertation wurde am 14.04.2015 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 03.08.2015 angenommen. Table of contents List of figures .................................................................................................................... iv List of tables ..................................................................................................................... vi Abbreviations .................................................................................................................. vii List of publications and contributions .............................................................................. viii Publications in peer-reviewed journals .................................................................................... viii My contributions to the publications ....................................................................................... viii Abstract -
Draft Genome Sequence of Aurantimonas Coralicida DM33-3 Isolated from Amundsen Sea Polynya
Korean Journal of Microbiology (2021) Vol. 57, No. 2, pp. 116-118 pISSN 0440-2413 DOI https://doi.org/10.7845/kjm.2021.1024 eISSN 2383-9902 Copyright ⓒ 2021, The Microbiological Society of Korea Draft genome sequence of Aurantimonas coralicida DM33-3 isolated from Amundsen Sea Polynya So-Jeong Kim1* , Jong-Geol Kim2, Gi-Yong Jung1, Jisoo Park3, and Eun-Jin Yang3 1Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Republic of Korea 2Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan 54538, Republic of Korea 3Division of Polar Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea 아문젠해 폴리냐로부터 분리된 Aurantimonas coralicida DM33-3의 유전체 분석 김소정1* ・ 김종걸2 ・ 정기용1 ・ 박지수3 ・ 양은진3 1한국지질자원연구원 지질환경연구본부, 2원광대학교 생명과학부, 3극지연구소 해양연구본부 (Received April 6, 2021; Revised May 12, 2021; Accepted June 1, 2021) Here, we report the draft genome sequence of Aurantimonas Aurantimonas manganoxydans SI85-9A1, is a known hetero- coralicida DM33-3 isolated from Amundsen Sea Polynya. The trophic Mn(II) oxidizer that produces Mn(III/IV) oxides (Dick genome size is 4,620,302 bp, 4,415 coding sequences, one et al., 2008). The genus Aurantimonas has been isolated from rRNA operon (additionally two 5S ribosomal RNA genes), and various environments such as deep-sea sediment (Li et al., 45 tRNA genes. Genes related to manganese oxidation and 2017), marine (Anderson et al., 2009), cave (Jurado et al., thiosulfate oxidation are also included in the genome. The genome harbors genes coding for enzymes having varying 2006), coral (Denner et al., 2003), root (Liu et al., 2016), and affinities to oxygen and nitrate reduction. -
1186713.2012.Pdf (3.835Mb)
BUSQUEDA DE RELACIONES ENTRE LA COMUNICACIÓN CELULAR BACTERIANA EL POTENCIAL DE VIRULENCIA Y LA ESTRUCTURA DE LA COMUNIDAD BACTERIANA EN LA ENFERMEDAD DE LA PLAGA BLANCA TIPO II Anny Johanna Cárdenas Barbosa Universidad Nacional de Colombia Facultad de Ciencias, Maestría en Ciencias - Microbiología Bogotá, Colombia 2012 BUSQUEDA DE RELACIONES ENTRE LA COMUNICACIÓN CELULAR BACTERIANA EL POTENCIAL DE VIRULENCIA Y LA ESTRUCTURA DE LA COMUNIDAD BACTERIANA EN LA ENFERMEDAD DE LA PLAGA BLANCA TIPO II Anny Johanna Cárdenas Barbosa Tesis de grado para optar al título de Magister en Ciencias - Microbiología Directora: Catalina Arévalo Ferro Dr. Rer. Nat. Profesor Asociado Departamento de Biología Línea de Investigación Ecología microbiana Grupo de Investigación Comunicación y Comunidades Bacterianas Universidad Nacional de Colombia Maestría en Ciencias – Microbiología Facultad de Ciencias, Universidad Nacional de Colombia A mis papas por darme las mejores enseñanzas de la vida A Migue por su aliento y compresión en todo momento A mi hermano por su incondicional apoyo por sus consejos y sus valores A mi directora de tesis, la profe Catalina, de quién siempre seguiré aprendiendo A Martín por darme hermosos momentos cada día A mis amigos Sofi, Juan Pablo y Sebastián por hacer que este camino siempre estuviera lleno de alegría AGRADECIMIENTOS Quiero expresar mi más sincera gratitud a la profesora Catalina Arevalo Ferro por su gran incentivo, supervisión y paciencia para el desarrollo de esta tesis. A los profesores Hernando Valencia y Luis Fernando Cadavid por abrirme siempre las puertas de sus laboratorios incondicionalmente. A mis compañeros del grupo de Comunicación y Comunidades Bacterianas por su constante apoyo. -
Corals and Sponges Under the Light of the Holobiont Concept: How Microbiomes Underpin Our Understanding of Marine Ecosystems
fmars-08-698853 August 11, 2021 Time: 11:16 # 1 REVIEW published: 16 August 2021 doi: 10.3389/fmars.2021.698853 Corals and Sponges Under the Light of the Holobiont Concept: How Microbiomes Underpin Our Understanding of Marine Ecosystems Chloé Stévenne*†, Maud Micha*†, Jean-Christophe Plumier and Stéphane Roberty InBioS – Animal Physiology and Ecophysiology, Department of Biology, Ecology & Evolution, University of Liège, Liège, Belgium In the past 20 years, a new concept has slowly emerged and expanded to various domains of marine biology research: the holobiont. A holobiont describes the consortium formed by a eukaryotic host and its associated microorganisms including Edited by: bacteria, archaea, protists, microalgae, fungi, and viruses. From coral reefs to the Viola Liebich, deep-sea, symbiotic relationships and host–microbiome interactions are omnipresent Bremen Society for Natural Sciences, and central to the health of marine ecosystems. Studying marine organisms under Germany the light of the holobiont is a new paradigm that impacts many aspects of marine Reviewed by: Carlotta Nonnis Marzano, sciences. This approach is an innovative way of understanding the complex functioning University of Bari Aldo Moro, Italy of marine organisms, their evolution, their ecological roles within their ecosystems, and Maria Pia Miglietta, Texas A&M University at Galveston, their adaptation to face environmental changes. This review offers a broad insight into United States key concepts of holobiont studies and into the current knowledge of marine model *Correspondence: holobionts. Firstly, the history of the holobiont concept and the expansion of its use Chloé Stévenne from evolutionary sciences to other fields of marine biology will be discussed. -
Aurantimonas Altamirensis Sp. Nov., a Member of the Order Rhizobiales Isolated from Altamira Cave
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC International Journal of Systematic and Evolutionary Microbiology (2006), 56, 2583–2585 DOI 10.1099/ijs.0.64397-0 Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from Altamira Cave Valme Jurado, Juan M. Gonzalez, Leonila Laiz and Cesareo Saiz-Jimenez Correspondence Instituto de Recursos Naturales y Agrobiologia, CSIC, Apartado 1052, 41080 Sevilla, Spain Juan M. Gonzalez [email protected] A bacterial strain, S21BT, was isolated from Altamira Cave (Cantabria, Spain). The cells were Gram- negative, short rods growing aerobically. Comparative 16S rRNA gene sequence analysis revealed that strain S21BT represented a separate subline of descent within the family ‘Aurantimonadaceae’ (showing 96 % sequence similarity to Aurantimonas coralicida) in the order Rhizobiales (Alphaproteobacteria). The major fatty acids detected were C16 : 0 and C18 : 1v7c. The G+C content of the DNA from strain S21BT was 71?8 mol%. Oxidase and catalase activities were present. Strain S21BT utilized a wide range of substrates for growth. On the basis of the results of this polyphasic study, isolate S21BT represents a novel species of the genus Aurantimonas, for which the name Aurantimonas altamirensis sp. nov. is proposed. The type strain is S21BT (=CECT 7138T=LMG 23375T). The genera Aurantimonas and Fulvimarina constitute Analysis of 16S rRNA gene sequences revealed that strain the two members of the recently described family S21BT belongs to the family ‘Aurantimonadaceae’ and is ‘Aurantimonadaceae’ within the order Rhizobiales. Both closely related to the members of the genera Aurantimonas genera are represented by single species, Aurantimonas (96?1 % similarity) and Fulvimarina (93?2 % similarity). -
First Case of Biliary Aureimonas Altamirensis Infection in a Patient
Infectious Diseases Research 1 First case of biliary Aureimonas altamirensis infection in a patient with colon cancer in China San-Tao Zhao, Wan-Shan Chen, Yun Lan, Mei-Jun Chen, Jian-Ping Li, Yu-Juan Guan, Feng-Yu Hu, Feng Li, Xiao-Ping Tang, and Ling-Hua Li Abstract—Aureimonas altamirensis, first reported in 2006, is China. This study was approved by the Institutional Review an aerobic, gram-negative bacillus. It is usually considered a Board of Guangzhou Eighth People’s Hospital (GZEH) and contaminant from the surrounding environment; however, recent informed consent of the patient was not required, considering evidences suggest that it may be an opportunistic pathogen in humans, which may cause multiple-site infections. Here, the low ethical load (IRB No.201817108). we report the first case of biliary A. altamirensis infection A 37-year-old man was admitted to GZEH in February in a patient with colon cancer in Guangzhou, China. The A. 2019, due to abnormal liver function. On admission, the patient altamirensis strain GZ8HT01 was isolated from the bile culture complained of nausea, vomiting, inappetence, abdominal pain, taken from the patient and identified by 16S ribosomal RNA and urine darkening for 7 days after receiving postoperative gene sequencing. Additionally, the bacterial strain was sensitive to all antibiotics tested. The patient was effectively treated with chemotherapy with two targeted drugs (PD-1 and CTLA- imipenem-cilastatin. These findings are valuable for the early 4). The patient’s medical history showed that he was diag- diagnosis and effective treatment of this emerging pathogen. nosed with descending colon cancer in 2016, but did not Key words: Aureimonas altamirensis, Biliary tract infection, have hepatitis or any other chronic liver disease. -
Jiella Aquimaris Gen. Nov., Sp. Nov., Isolated from Offshore Surface Seawater
International Journal of Systematic and Evolutionary Microbiology (2015), 65, 1127–1132 DOI 10.1099/ijs.0.000067 Jiella aquimaris gen. nov., sp. nov., isolated from offshore surface seawater Jing Liang,1 Ji Liu1 and Xiao-Hua Zhang1,2 Correspondence 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China Xiao-Hua Zhang 2Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China [email protected] A Gram-stain-negative, strictly aerobic and rod-shaped motile bacterium with peritrichous flagella, designated strain LZB041T, was isolated from offshore surface seawater of the East China Sea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LZB041T formed a lineage within the family ‘Aurantimonadaceae’ that was distinct from the most closely related genera Aurantimonas (96.0–96.4 % 16S rRNA gene sequence similarity) and Aureimonas (94.5–96.0 %). Optimal growth occurred in the presence of 1–7 % (w/v) NaCl, at pH 7.0–8.0 and at 28–37 6C. Ubiquinone-10 was the predominant respiratory quinone. The major fatty acids (.10 % of total fatty acids) were C18 : 1v7c and/or C18 : 1v6c (summed feature 8) and cyclo- C19 : 0v8c. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphati- dylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, one unknown aminolipid, one unknown phospholipid and one unknown polar lipid. The DNA G+C content of strain LZB041T was 71.3 mol%. On the basis of polyphasic analysis, strain LZB041T is considered to represent a novel species of a new genus in the class Alphaproteobacteria, for which the name Jiella aquimaris gen. -
Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju. -
Characterization and Comparison of Intestinal Bacterial Microbiomes of Euschistus Heros and Piezodorus Guildinii Collected in Brazil and the United States
Characterization and Comparison of Intestinal Bacterial Microbiomes of Euschistus Heros and Piezodorus Guildinii Collected in Brazil and the United States Matheus Sartori Moro ( [email protected] ) State University of Campinas, Campinas (UNICAMP), Piracicaba, SP – Brazil https://orcid.org/0000- 0003-0266-521X Xing Wu Yale University Wei Wei University of Illinois at Urbana-Champaign Lucas William Mendes Universidade de São Paulo Centro de Energia Nuclear na Agricultura: Universidade de Sao Paulo Centro de Energia Nuclear na Agricultura Clint Allen USDA Agricultural Research Service José Baldin Pinheiro ESALQ-USP: Universidade de Sao Paulo Escola Superior de Agricultura Luiz de Queiroz Steven John Clough University of Illinois at Urbana-Champaign Maria Imaculada Zucchi APTA: Agencia Paulista de Tecnologia dos Agronegocios Research Keywords: Distribution, Glycine max, insect pests, microora, stink bugs Posted Date: January 20th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-149489/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/25 Abstract Background: Herbaceous insects are one of the main biological threats to crops. One such group of insects, stink bugs, do not eat large amounts of tissue when feeding on soybean, but are extremely damaging to the quality of the seed yield as they feed directly on green developing seeds leading to poorly marketable harvests. In addition to causing physical damage to the seed during feeding, the insects can also transmit microbial pathogens, leading to even greater yield loss. Conducting surveys of the insect intestinal microbiome can help identify possible pathogens, as well as detail what healthy stink bug digestive systems have in common. -
Molecular Phylogeny and Biotechnological Potential of Bacterial Endophytes Associated with Malpighia Emarginata
Molecular phylogeny and biotechnological potential of bacterial endophytes associated with Malpighia emarginata V. Specian1, A.T. Costa1, A.C. Felber1, J.C. Polonio1, J.L. Azevedo2 and J.A. Pamphile1 1Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, PR, Brasil 2Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP, Brasil Corresponding author: J.A. Pamphile E-mail: [email protected] Genet. Mol. Res. 15 (2): gmr.15027777 Received October 5, 2015 Accepted December 3, 2015 Published April 26, 2016 DOI http://dx.doi.org/10.4238/gmr.15027777 ABSTRACT. Acerola (Malpighia emarginata) is a shrub native to tropical and subtropical climates, which has great commercial interest due to the high vitamin C content of its fruit. However, there are no reports of the endophytic community of this plant species. The aim of this study was to verify the genetic diversity of the leaf endophytic bacterial community of two varieties (Olivier & Waldy Cati 30) of acerola, and to evaluate their biotechnological ability by assessing their in vitro control of pathogenic fungi and the enzymatic production of cellulase, xylanase, amylase, pectinase, protease, lipase, esterase, and chitinase. In total, 157 endophytic bacteria were isolated from the leaves of two varieties of the plant at 28° and 37°C. Phylogenetic analysis confirmed the molecular identification of 58 bacteria, 39.65% of which were identified at the species level. For the first time, the genus Aureimonas was highlighted as an endophytic bacterium. Furthermore, 12.82% of the isolates inhibited the growth of all phytopathogens evaluated and Genetics and Molecular Research 15 (2): gmr.15027777 ©FUNPEC-RP www.funpecrp.com.br V.