Metaproteomics Characterization of the Alphaproteobacteria
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Deep Microbial Community Profiling Along the Fermentation Process of Pulque, a Major Biocultural Resource of Mexico
bioRxiv preprint doi: https://doi.org/10.1101/718999; this version posted July 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico. 1 1 2 Carolina Rocha-Arriaga , Annie Espinal-Centeno , Shamayim Martinez-Sanchez , Juan 1 2 1,3 Caballero-Pérez , Luis D. Alcaraz * & Alfredo Cruz-Ramirez *. 1 Molecular & Developmental Complexity Group, Unit of Advanced Genomics, LANGEBIO-CINVESTAV, Irapuato, México. 2 Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Cd. Universitaria, 04510 Coyoacán, Mexico City, Mexico. 3 Escuela de Agronomía, Universidad de La Salle Bajío, León, Gto, Mexico. *Corresponding authors: [email protected], [email protected] ● Our approach allowed the identification of a broader microbial diversity in Pulque ● We increased 4.4 times bacteria genera and 40 times fungal species detected in mead. ● Newly reported bacteria genera and fungal species associated to Pulque fermentation Abstract Some of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. During colonial times they were renamed with the antillan word maguey. This was changed again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several Mexican prehispanic cultures, Agave species were not only considered as crops, but also part of their biocultural resources and cosmovision. Among the major products obtained from some Agave spp since pre-hispanic times is the alcoholic beverage called pulque or octli. -
Endobacter Medicaginis Gen. Nov. Sp. Nov. Isolated from Alfalfa Nodules In
IJSEM Papers in Press. Published September 21, 2012 as doi:10.1099/ijs.0.041368-0 1 Endobacter medicaginis gen. nov. sp. nov. isolated from alfalfa nodules in an acidic 2 soil in Spain 3 4 Martha Helena Ramírez-Bahena1,2, Carmen Tejedor3, Isidro Martín3, Encarna 5 Velázquez2, 3, Alvaro Peix1,2* 6 7 8 1: Instituto de Recursos Naturales y Agrobiología de Salamanca. Consejo Superior de 9 Investigaciones Científicas. (IRNASA-CSIC). Salamanca. Spain. 10 2: Unidad Asociada Grupo de Interacciones planta-microorganismo Universidad de 11 Salamanca-IRNASA (CSIC). Salamanca. Spain 12 3: Departamento de Microbiología y Genética. Universidad de Salamanca. Salamanca. 13 Spain 14 15 16 17 18 Running title: Endobacter medicaginis gen. nov. sp. nov. 19 20 Abstract 21 A bacterial strain designed M1MS02T was isolated from a surface sterilised nodule of 22 Medicago sativa in Zamora (Spain). The 16S rRNA gene sequence of this strain showed 23 96.5 and 96.2% identities, respectively, with respect to Gluconacetobacter liquefaciens 24 IFO 12388T and Granulibacter bethesdensis CGDNIH1T from the Family 25 Acetobacteraceae. The isolate was Gram negative, non-sporulated aerobic motile by a 26 subpolar flagellum coccoid to rod-shaped bacterium. Major fatty acid is C18:1 7c 27 (39.94%) and major ubiquinone is Q-10. The lipid profile consisted of 28 diphosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, three 29 aminolipids, four glycolipids, two phospholipids and a lipid. Catalase positive and 30 oxidase and urease negative. Acetate and lactate are not oxydized. Acetic acid is 31 produced from ethanol in culture media supplemented with 2% CaCO3. Ammonium 32 sulphate is assimilated in glucose medium. -
Community Analysis of Microbial Sharing and Specialization in A
Downloaded from http://rspb.royalsocietypublishing.org/ on March 15, 2017 Community analysis of microbial sharing rspb.royalsocietypublishing.org and specialization in a Costa Rican ant–plant–hemipteran symbiosis Elizabeth G. Pringle1,2 and Corrie S. Moreau3 Research 1Department of Biology, Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Cite this article: Pringle EG, Moreau CS. 2017 Reno, NV 89557, USA 2Michigan Society of Fellows, University of Michigan, Ann Arbor, MI 48109, USA Community analysis of microbial sharing and 3Department of Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, specialization in a Costa Rican ant–plant– Chicago, IL 60605, USA hemipteran symbiosis. Proc. R. Soc. B 284: EGP, 0000-0002-4398-9272 20162770. http://dx.doi.org/10.1098/rspb.2016.2770 Ants have long been renowned for their intimate mutualisms with tropho- bionts and plants and more recently appreciated for their widespread and diverse interactions with microbes. An open question in symbiosis research is the extent to which environmental influence, including the exchange of Received: 14 December 2016 microbes between interacting macroorganisms, affects the composition and Accepted: 17 January 2017 function of symbiotic microbial communities. Here we approached this ques- tion by investigating symbiosis within symbiosis. Ant–plant–hemipteran symbioses are hallmarks of tropical ecosystems that produce persistent close contact among the macroorganism partners, which then have substantial opportunity to exchange symbiotic microbes. We used metabarcoding and Subject Category: quantitative PCR to examine community structure of both bacteria and Ecology fungi in a Neotropical ant–plant–scale-insect symbiosis. Both phloem-feed- ing scale insects and honeydew-feeding ants make use of microbial Subject Areas: symbionts to subsist on phloem-derived diets of suboptimal nutritional qual- ecology, evolution, microbiology ity. -
Case Report: Dermanyssus Gallinae in a Patient with Pruritus and Skin Lesions
Türkiye Parazitoloji Dergisi, 33 (3): 242 - 244, 2009 Türkiye Parazitol Derg. © Türkiye Parazitoloji Derneği © Turkish Society for Parasitology Case Report: Dermanyssus gallinae in a Patient with Pruritus and Skin Lesions Cihangir AKDEMİR1, Erim GÜLCAN2, Pınar TANRITANIR3 Dumlupinar University, School of Medicine 1Department of Parasitology, 2Department of Internal Medicine, Kütahya, 3Yuzuncu Yil University, College of Health, Van, Türkiye SUMMARY: A 40-year old woman patient who presented at the Dumlupınar University Faculty of Medicine Hospital reported intensi- fied itching on her body during evening hours. During her physical examination, puritic dermatitis lesions were found on the patient's shoulders, neck and arms in particular, and systemic examination and labaratory tests were found to be normal. The patient's story showed that similar signs had been seen in other members of the household. They reside on the top floor of a building and pigeons are occasionally seen in the ventilation shaft. Examination of the house was made. The walls of the house, door architraves and finally beds, sheets and blankets and the windows opening to the outside were examined. During the examination, arthropoda smaller than 1 mm were detected. Following preparation of the collected samples, these were found to be Dermanyssus gallinae. Together with this presentation of this event, it is believed cutaneus reactions stemming from birds could be missed and that whether or not of pets or wild birds exist in or around the homes should be investigated. Key Words: Pruritus, itching, dermatitis, skin lesions, Dermanyssus gallinae Olgu Sunumu: Prüritus ve Deri Lezyonlu Bir Hastada Dermanyssus gallinae ÖZET: Dumlupınar Üniversitesi Tıp Fakültesi Hastanesine müracaat eden 40 yaşındaki kadın hasta, vücudunda akşam saatlerinde yo- ğunlaşan kaşıntı şikayetlerini bildirmiştir. -
Protein Expression Profile of Gluconacetobacter Diazotrophicus PAL5, a Sugarcane Endophytic Plant Growth-Promoting Bacterium
Proteomics 2008, 8, 1631–1644 DOI 10.1002/pmic.200700912 1631 RESEARCH ARTICLE Protein expression profile of Gluconacetobacter diazotrophicus PAL5, a sugarcane endophytic plant growth-promoting bacterium Leticia M. S. Lery1, 2, Ana Coelho1, 3, Wanda M. A. von Kruger1, 2, Mayla S. M. Gonc¸alves1, 3, Marise F. Santos1, 4, Richard H. Valente1, 5, Eidy O. Santos1, 3, Surza L. G. Rocha1, 5, Jonas Perales1, 5, Gilberto B. Domont1, 4, Katia R. S. Teixeira1, 6 and Paulo M. Bisch1, 2 1 Rio de Janeiro Proteomics Network, Rio de Janeiro, Brazil 2 Unidade Multidisciplinar de Genômica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil 3 Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil 4 Laboratório de Química de Proteínas, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil 5 Laboratório de Toxinologia, Departamento de Fisiologia e Farmacodinâmica- Instituto Oswaldo Cruz- Fundac¸ão Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil 6 Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, Seropédica, Brazil This is the first broad proteomic description of Gluconacetobacter diazotrophicus, an endophytic Received: September 25, 2007 bacterium, responsible for the major fraction of the atmospheric nitrogen fixed in sugarcane in Revised: December 18, 2007 tropical regions. Proteomic coverage of G. diazotrophicus PAL5 was obtained by two independent Accepted: December 19, 2007 approaches: 2-DE followed by MALDI-TOF or TOF-TOF MS and 1-DE followed by chromatog- raphy in a C18 column online coupled to an ESI-Q-TOF or ESI-IT mass spectrometer. -
Reconstructing the Origin of Oxygenic Photosynthesis: Do Assembly and Photoactivation Recapitulate Evolution?
HYPOTHESIS AND THEORY published: 02 March 2016 doi: 10.3389/fpls.2016.00257 Reconstructing the Origin of Oxygenic Photosynthesis: Do Assembly and Photoactivation Recapitulate Evolution? Tanai Cardona * Department of Life Sciences, Imperial College London, London, UK Due to the great abundance of genomes and protein structures that today span a broad diversity of organisms, now more than ever before, it is possible to reconstruct the molecular evolution of protein complexes at an incredible level of detail. Here, I recount the story of oxygenic photosynthesis or how an ancestral reaction center was transformed into a sophisticated photochemical machine capable of water oxidation. First, I review the evolution of all reaction center proteins in order to highlight that Photosystem II and Photosystem I, today only found in the phylum Cyanobacteria, branched out very early in the history of photosynthesis. Therefore, it is very unlikely that they were acquired via horizontal gene transfer from any of the described phyla of Edited by: anoxygenic phototrophic bacteria. Second, I present a new evolutionary scenario for the Julian Eaton-Rye, origin of the CP43 and CP47 antenna of Photosystem II. I suggest that the antenna University of Otago, New Zealand proteins originated from the remodeling of an entire Type I reaction center protein and Reviewed by: Anthony William Larkum, not from the partial gene duplication of a Type I reaction center gene. Third, I highlight University of Technology, Sydney, how Photosystem II and Photosystem I reaction center proteins interact with small Australia Martin Hohmann-Marriott, peripheral subunits in remarkably similar patterns and hypothesize that some of this Norwegian University of Science and complexity may be traced back to the most ancestral reaction center. -
Reclassification of Agrobacterium Ferrugineum LMG 128 As Hoeflea
International Journal of Systematic and Evolutionary Microbiology (2005), 55, 1163–1166 DOI 10.1099/ijs.0.63291-0 Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov. Alvaro Peix,1 Rau´l Rivas,2 Martha E. Trujillo,2 Marc Vancanneyt,3 Encarna Vela´zquez2 and Anne Willems3 Correspondence 1Departamento de Produccio´n Vegetal, Instituto de Recursos Naturales y Agrobiologı´a, Encarna Vela´zquez IRNA-CSIC, Spain [email protected] 2Departamento de Microbiologı´a y Gene´tica, Lab. 209, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain 3Laboratory of Microbiology, Dept Biochemistry, Physiology and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium Members of the species Agrobacterium ferrugineum were isolated from marine environments. The type strain of this species (=LMG 22047T=ATCC 25652T) was recently reclassified in the new genus Pseudorhodobacter, in the order ‘Rhodobacterales’ of the class ‘Alphaproteobacteria’. Strain LMG 128 (=ATCC 25654) was also initially classified as belonging to the species Agrobacterium ferrugineum; however, the nearly complete 16S rRNA gene sequence of this strain indicated that it does not belong within the genus Agrobacterium or within the genus Pseudorhodobacter. The closest related organism, with 95?5 % 16S rRNA gene similarity, was Aquamicrobium defluvii from the family ‘Phyllobacteriaceae’ in the order ‘Rhizobiales’. The remaining genera from this order had 16S rRNA gene sequence similarities that were lower than 95?1 % with respect to strain LMG 128. These phylogenetic distances suggested that strain LMG 128 belonged to a different genus. The major fatty acid present in strain LMG 128 was mono-unsaturated straight chain 18 : 1v7c. -
Community Structure and Function of High-Temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments
ORIGINAL RESEARCH ARTICLE published: 03 June 2013 doi: 10.3389/fmicb.2013.00106 Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments Christian G. Klatt 1,2†,William P.Inskeep 1,2*, Markus J. Herrgard 3, Zackary J. Jay 1,2, Douglas B. Rusch4, Susannah G.Tringe 5, M. Niki Parenteau 6,7, David M. Ward 1,2, Sarah M. Boomer 8, Donald A. Bryant 9,10 and Scott R. Miller 11 1 Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA 2 Thermal Biology Institute, Montana State University, Bozeman, MT, USA 3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark 4 Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA 5 Department of Energy Joint Genome Institute, Walnut Creek, CA, USA 6 Search for Extraterrestrial Intelligence Institute, Mountain View, CA, USA 7 National Aeronautics and Space Administration Ames Research Center, Mountain View, CA, USA 8 Western Oregon University, Monmouth, OR, USA 9 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA 10 Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA 11 Department of Biological Sciences, University of Montana, Missoula, MT, USA Edited by: Six phototrophic microbial mat communities from different geothermal springs (YNP) were Martin G. Klotz, University of North studied using metagenome sequencing and geochemical analyses. The primary goals of Carolina at Charlotte, USA this work were to determine differences in community composition of high-temperature Reviewed by: Andreas Teske, University of North phototrophic mats distributed across theYellowstone geothermal ecosystem, and to iden- Carolina at Chapel Hill, USA tify metabolic attributes of predominant organisms present in these communities that may Jesse Dillon, California State correlate with environmental attributes important in niche differentiation. -
Mesostigmata: Dermanyssidae), in Laboratory and Field Trials*
35-Liebisch et al-AF:35-Liebisch et al-AF 11/25/11 2:52 AM Page 282 Zoosymposia 6: 282–287 (2011) ISSN 1178-9905 (print edition) www.mapress.com/zoosymposia/ ZOOSYMPOSIA Copyright © 2011 . Magnolia Press ISSN 1178-9913 (online edition) Efficacy of spinosad against the poultry red mite, Dermanyssus gallinae (Mesostigmata: Dermanyssidae), in laboratory and field trials* GABRIELE LIEBISCH, RICHARD HACK & GOSSE SMID Laboratorium für klinische Diagnostik ZeckLab, Up’n Kampe 3, D-30938, Germany * In: Moraes, G.J. de & Proctor, H. (eds) Acarology XIII: Proceedings of the International Congress. Zoosymposia, 6, 1–304. Abstract The poultry red mite, Dermanyssus gallinae (De Geer), is the most economically important ectoparasite in poultry houses in many countries around the world. The lack of efficacy of commercial products in its control results from poor application and/or from its resistance to active ingredients. A new insecticide, spinosad, was tested against mobi - le stages of the red mite in laboratory and field populations. Laboratory trials showed increasing efficacy five days (adults) and six days (nymphs) after exposure. Laboratory results were confirmed in a field trial conducted under com - mercial conditions. The trial was conducted in three separate houses on farms with high natural mite populations. The first and second houses were sprayed with concentrations of 2,000 and 4,000 ppm of spinosad (2 and 4 g/L), whereas the third house was used as an untreated control. Spraying was conducted using a sprayer (Stadikopumpe VA AR 252- 200 LE, Dinklage, Germany) with a 200 L reservoir with permanent stirring, a 50 m long flexible tube with a double jet system, and jet size of 0.08 mm. -
Dissertation Implementing Organic Amendments To
DISSERTATION IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE Submitted by Erika J. Foster Graduate Degree Program in Ecology In partial fulfillment of the requirements For the Degree of Doctor of Philosophy Colorado State University Fort Collins, Colorado Summer 2018 Doctoral Committee: Advisor: M. Francesca Cotrufo Louise Comas Charles Rhoades Matthew D. Wallenstein Copyright by Erika J. Foster 2018 All Rights Reserved i ABSTRACT IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE To sustain agricultural production into the future, management should enhance natural biogeochemical cycling within the soil. Strategies to increase yield while reducing chemical fertilizer inputs and irrigation require robust research and development before widespread implementation. Current innovations in crop production use amendments such as manure and biochar charcoal to increase soil organic matter and improve soil structure, water, and nutrient content. Organic amendments also provide substrate and habitat for soil microorganisms that can play a key role cycling nutrients, improving nutrient availability for crops. Additional plant growth promoting bacteria can be incorporated into the soil as inocula to enhance soil nutrient cycling through mechanisms like phosphorus solubilization. Since microbial inoculation is highly effective under drought conditions, this technique pairs well in agricultural systems using limited irrigation to save water, particularly in semi-arid regions where climate change and population growth exacerbate water scarcity. The research in this dissertation examines synergistic techniques to reduce irrigation inputs, while building soil organic matter, and promoting natural microbial function to increase crop available nutrients. The research was conducted on conventional irrigated maize systems at the Agricultural Research Development and Education Center north of Fort Collins, CO. -
(Antarctica) Glacial, Basal, and Accretion Ice
CHARACTERIZATION OF ORGANISMS IN VOSTOK (ANTARCTICA) GLACIAL, BASAL, AND ACCRETION ICE Colby J. Gura A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 2019 Committee: Scott O. Rogers, Advisor Helen Michaels Paul Morris © 2019 Colby Gura All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Chapter 1: Lake Vostok is named for the nearby Vostok Station located at 78°28’S, 106°48’E and at an elevation of 3,488 m. The lake is covered by a glacier that is approximately 4 km thick and comprised of 4 different types of ice: meteoric, basal, type 1 accretion ice, and type 2 accretion ice. Six samples were derived from the glacial, basal, and accretion ice of the 5G ice core (depths of 2,149 m; 3,501 m; 3,520 m; 3,540 m; 3,569 m; and 3,585 m) and prepared through several processes. The RNA and DNA were extracted from ultracentrifugally concentrated meltwater samples. From the extracted RNA, cDNA was synthesized so the samples could be further manipulated. Both the cDNA and the DNA were amplified through polymerase chain reaction. Ion Torrent primers were attached to the DNA and cDNA and then prepared to be sequenced. Following sequencing the sequences were analyzed using BLAST. Python and Biopython were then used to collect more data and organize the data for manual curation and analysis. Chapter 2: As a result of the glacier and its geographic location, Lake Vostok is an extreme and unique environment that is often compared to Jupiter’s ice-covered moon, Europa. -
Extended Evaluation of Viral Diversity in Lake Baikal Through Metagenomics
microorganisms Article Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics Tatyana V. Butina 1,* , Yurij S. Bukin 1,*, Ivan S. Petrushin 1 , Alexey E. Tupikin 2, Marsel R. Kabilov 2 and Sergey I. Belikov 1 1 Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; [email protected] (I.S.P.); [email protected] (S.I.B.) 2 Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; [email protected] (A.E.T.); [email protected] (M.R.K.) * Correspondence: [email protected] (T.V.B.); [email protected] (Y.S.B.) Abstract: Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake’s viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previ- ously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still un- Citation: Butina, T.V.; Bukin, Y.S.; Petrushin, I.S.; Tupikin, A.E.; Kabilov, known.