Effect of Transient Exposure to Carbaryl Wettable Powder on the Gut
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Genomic Diversity Landscape of the Honey Bee Gut Microbiota
ARTICLE https://doi.org/10.1038/s41467-019-08303-0 OPEN Genomic diversity landscape of the honey bee gut microbiota Kirsten M. Ellegaard 1 & Philipp Engel 1 The structure and distribution of genomic diversity in natural microbial communities is largely unexplored. Here, we used shotgun metagenomics to assess the diversity of the honey bee gut microbiota, a community consisting of few bacterial phylotypes. Our results show that 1234567890():,; most phylotypes are composed of sequence-discrete populations, which co-exist in individual bees and show age-specific abundance profiles. In contrast, strains present within these sequence-discrete populations were found to segregate into individual bees. Consequently, despite a conserved phylotype composition, each honey bee harbors a distinct community at the functional level. While ecological differentiation seems to facilitate coexistence at higher taxonomic levels, our findings suggest that, at the level of strains, priority effects during community assembly result in individualized profiles, despite the social lifestyle of the host. Our study underscores the need to move beyond phylotype-level characterizations to understand the function of this community, and illustrates its potential for strain-level analysis. 1 Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland. Correspondence and requests for materials should be addressed to K.M.E. (email: [email protected]) or to P.E. (email: [email protected]) NATURE COMMUNICATIONS | (2019) 10:446 | https://doi.org/10.1038/s41467-019-08303-0 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-08303-0 ost bacteria live in genetically diverse and highly com- same species name22. -
JMBFS / Surname of Author Et Al. 20Xx X (X) X-Xx
DIVERSITY OF BACTERIA IN SLOVAK AND FOREIGN HONEY, WITH ASSESSMENT OF ITS PHYSICO- CHEMICAL QUALITY AND COUNTS OF CULTIVABLE MICROORGANISMS Vladimíra Kňazovická1, Michal Gábor2, Martina Miluchová2, Marek Bobko3, Juraj Medo*4 Address(es): Ing. Juraj Medo, PhD. 1National Agricultural and Food Centre, Research Institute for Animal Production Nitra, Institute of Apiculture Liptovsky Hradok, Gasperikova 599, 033 80 Liptovsky Hradok, Slovakia. 2Slovak University of Agriculture in Nitra, Faculty of Agrobiology and Food Resources, Department of Genetics and Animal Breeding Biology, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia. 3Slovak University of Agriculture in Nitra, Faculty of Biotechnology and Food Sciences, Department of Technology and Quality of Animal Products, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia. 4Slovak University of Agriculture in Nitra, Faculty of Biotechnology and Food Sciences, Department of Microbiology, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia, phone number: +421 37 641 5810. *Corresponding author: [email protected] doi: 10.15414/jmbfs.2019.9.special.414-421 ARTICLE INFO ABSTRACT Received 23. 8. 2019 The aim of the study was to assess microbial microbiome of 30 honey samples and compare potential differences between the samples Revised 7. 10. 2019 from apiaries and commercial trade in Slovakia and foreign countries (Latvia, Switzerland, India, Japan and Tanzania) as well as to Accepted 10. 10. 2019 indicate their physico-chemical and basic microbiological quality. Study of each sample consisted of physico-chemical analysis (water Published 8. 11. 2019 content, pH, free acidity and electrical conductivity), basic microbiological analysis performed by dilution plating method (total plate count, sporulating aerobic microorganisms, bacteria from Enterobacteriaceae family, preliminary lactic acid bacteria and microscopic fungi) and metagenomic analysis for bacterial diversity evaluation. -
Lists of Names of Prokaryotic Candidatus Taxa
NOTIFICATION LIST: CANDIDATUS LIST NO. 1 Oren et al., Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.003789 Lists of names of prokaryotic Candidatus taxa Aharon Oren1,*, George M. Garrity2,3, Charles T. Parker3, Maria Chuvochina4 and Martha E. Trujillo5 Abstract We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, pro- posed between the mid- 1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evo- lutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current propos- als to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes. Introduction of the category called Candidatus was first pro- morphology, basis of assignment as Candidatus, habitat, posed by Murray and Schleifer in 1994 [1]. The provisional metabolism and more. However, no such lists have yet been status Candidatus was intended for putative taxa of any rank published in the journal. that could not be described in sufficient details to warrant Currently, the nomenclature of Candidatus taxa is not covered establishment of a novel taxon, usually because of the absence by the rules of the Prokaryotic Code. -
The Bumble Bee Microbiome Increases Survival of Bees Exposed to Selenate Toxicity
Full Title The bumble bee microbiome increases survival of bees exposed to selenate toxicity. Running title The microbiome increases survival of selenate-exposed bumble bees. Jason A. Rothmanab, Laura Legerb, Peter Graystockbc, Kaleigh Russellb, and Quinn S. McFrederickab# a. Graduate Program in Microbiology, University of California, Riverside, CA 92521, USA b. Department of Entomology, University of California, Riverside, CA, 92521, USA c. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK # Corresponding Author: Department of Entomology, 900 University Ave., University of California, Riverside, CA 92521, [email protected], (951) 827-5817 Competing Interests The authors declare that we have no competing interests. This research was supported by Initial Complement funds and NIFA Hatch funds (CA-R-ENT-5109-H) from UC Riverside to Quinn McFrederick and through fellowships awarded to Jason A. Rothman by the National Aeronautics This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/1462-2920.14641 This article is protected by copyright. All rights reserved. and Space Administration MIRO Fellowships in Extremely Large Data Sets (Award No: NNX15AP99A) and the United States Department of Agriculture National Institute of Food and Agriculture Predoctoral Fellowship (Award No. 2018-67011-28123). This article is protected by copyright. All rights reserved. Originality-Significance Statement The symbiotic microbiome of insects has been implicated in pathogen defense, nutrient digestion, immune signaling and toxicant mitigation. -
Common Structuring Principles of the Drosophila Melanogaster Microbiome on a Continental Scale and Between Host and Substrate
Environmental Microbiology Reports (2020) 12(2), 220–228 doi:10.1111/1758-2229.12826 Brief Report Common structuring principles of the Drosophila melanogaster microbiome on a continental scale and between host and substrate Yun Wang, 1,2 Martin Kapun, 1,3,4 Lena Waidele, 1,2 Introduction Sven Kuenzel,5 Alan O. Bergland 1,6 and Environmental factors and stochastic processes play Fabian Staubach 1,2* important roles in shaping microbiomes (Spor et al., 1The European Drosophila Population Genomics 2011; van Opstal and Bordenstein, 2015). Recent data Consortium (DrosEU). across a variety of hosts, including mammals and 2Department of Evolutionary Biology and Animal insects, suggest that environmental factors like host diet Ecology, Biology I, University of Freiburg, Freiburg im often have a dominant effect on microbiome composition Breisgau, Germany. (Chandler et al., 2011; Wu et al., 2011; Staubach et al., 3Department of Evolutionary Biology and Environmental 2013; Wang et al., 2014; Waidele et al., 2017; Rothschild Studies, University of Zürich, Zürich, Switzerland. 4Department of Cell and Developmental Biology, et al., 2018). In order to explain variation between Medical University of Vienna, Vienna, Austria. microbiomes from the same species, stochastic, ecologi- 5Max Planck Institute for Evolutionary Biology, Plön, cally neutral processes have moved into focus. These Germany. processes comprise ecological drift, dispersal and coloni- 6Department of Biology, University of Virginia, zation history. It appears plausible for diverse species Charlottesville, VA, USA. (Sieber et al., 2019), including Drosophila (Adair et al., 2018) that neutral processes dominate microbiome assembly. Summary The ability of D. melanogaster to shape its associated The relative importance of host control, environmental microbiome might be limited (Blum et al., 2013; Wong effects and stochasticity in the assemblage of host- et al., 2013). -
Bacterial Diversity Shift Determined by Different Diets in the Gut of the Spotted Wing Fly Drosophila Suzukii Is Primarily Reflected on Acetic Acid Bacteria
Bacterial diversity shift determined by different diets in the gut of the spotted wing fly Drosophila suzukii is primarily reflected on acetic acid bacteria Item Type Article Authors Vacchini, Violetta; Gonella, Elena; Crotti, Elena; Prosdocimi, Erica M.; Mazzetto, Fabio; Chouaia, Bessem; Callegari, Matteo; Mapelli, Francesca; Mandrioli, Mauro; Alma, Alberto; Daffonchio, Daniele Citation Vacchini V, Gonella E, Crotti E, Prosdocimi EM, Mazzetto F, et al. (2016) Bacterial diversity shift determined by different diets in the gut of the spotted wing fly Drosophila suzukii is primarily reflected on acetic acid bacteria. Environmental Microbiology Reports. Available: http://dx.doi.org/10.1111/1758-2229.12505. Eprint version Post-print DOI 10.1111/1758-2229.12505 Publisher Wiley Journal Environmental Microbiology Reports Rights This is the peer reviewed version of the following article: Vacchini, V., Gonella, E., Crotti, E., Prosdocimi, E. M., Mazzetto, F., Chouaia, B., Callegari, M., Mapelli, F., Mandrioli, M., Alma, A. and Daffonchio, D. (2016), Bacterial diversity shift determined by different diets in the gut of the spotted wing fly Drosophila suzukii is primarily reflected on acetic acid bacteria. Environmental Microbiology Reports. Accepted Author Manuscript. doi:10.1111/1758-2229.12505, which has been published in final form at http://onlinelibrary.wiley.com/ doi/10.1111/1758-2229.12505/abstract. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving. Download date 02/10/2021 16:15:24 Link to Item http://hdl.handle.net/10754/622736 Bacterial diversity shift determined by different diets in the gut of the spotted wing fly Drosophila suzukii is primarily reflected on acetic acid bacteria Violetta Vacchini1#, Elena Gonella2#, Elena Crotti1#, Erica M. -
A Higher Level Classification of All Living Organisms
RESEARCH ARTICLE A Higher Level Classification of All Living Organisms Michael A. Ruggiero1*, Dennis P. Gordon2, Thomas M. Orrell1, Nicolas Bailly3, Thierry Bourgoin4, Richard C. Brusca5, Thomas Cavalier-Smith6, Michael D. Guiry7, Paul M. Kirk8 1 Integrated Taxonomic Information System, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America, 2 National Institute of Water & Atmospheric Research, Wellington, New Zealand, 3 WorldFish—FIN, Los Baños, Philippines, 4 Institut Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 MNHN-CNRS-UPMC-EPHE, Sorbonne Universités, Museum National d'Histoire Naturelle, 57, rue Cuvier, CP 50, F-75005, Paris, France, 5 Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America, 6 Department of Zoology, University of Oxford, Oxford, United Kingdom, 7 The AlgaeBase Foundation & Irish Seaweed Research Group, Ryan Institute, National University of Ireland, Galway, Ireland, 8 Mycology Section, Royal Botanic Gardens, Kew, London, United Kingdom * [email protected] Abstract We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists’ expert opinions in a unified and coherent, OPEN ACCESS hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collab- orative effort is to provide a hierarchical classification serving not only the needs of the Citation: Ruggiero MA, Gordon DP, Orrell TM, Bailly CoL’s database providers but also the diverse public-domain user community, most of N, Bourgoin T, Brusca RC, et al. (2015) A Higher Level Classification of All Living Organisms. PLoS whom are familiar with the Linnaean conceptual system of ordering taxon relationships. -
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. -
Uludağ Arıcılık Dergisi 2020-1
Atıf/Citation: Bengü, AŞ., Kutlu, MA. 2020. Bingöl’den Temin Edilen Ballarda ICP-MS ile Bazı Temel ve Toksik Elementlerin Analizi (Analysis of Some Essential and Toxic Elements by ICP-MS in Honey Obtained from Bingol). U.Arı D.-U. Bee. J. 20(1): 1-12, DOI: 10.31467/uluaricilik.648631 ARAŞTIRMA MAKALESİ / RESEARCH ARTICLE BİNGÖL’DEN TEMİN EDİLEN BALLARDA ICP-MS İLE BAZI TEMEL VE TOKSİK ELEMENTLERİN ANALİZİ Analysis of Some Essential and Toxic Elements by ICP-MS in Honey Obtained from Bingol Aydın Şükrü BENGÜ1, Mehmet Ali KUTLU2 1Bingöl Üniversitesi Sağlık Hizmetleri MYO, TÜRKİYE, ORCID NO: 0000-0002-7635-4855, Yazışma Yazarı / Corresponding author: E-mail: [email protected] 2Bingöl Üniversitesi Teknik Bilimler Meslek Yüksek Okulu Arıcılık Programı, TÜRKİYE, ORCID NO: 0000-0003-0862- 9690, E-posta: [email protected] Geliş Tarihi / Received:11.11.2019 Kabul Tarihi / Accepted: 28.01.2020 DOI: 10.31467/uluaricilik.648631 ÖZET Araştırma Bingöl’de 2019 yılı bal hasat sonrası elde edilen süzme ballardaki bazı elementlerin ve ağır metallerin tespitine yönelik olarak yapılmıştır. Bal üretim alanlarından temin edilen 11 adet süzme bal örneklerinde bazı elementlerin ve ağır metallerin düzeyleri ICP-MS (İndüktif Eşleşmiş Plazma-Kütle Spektrometresi) ile belirlenmiştir. Bal örneklerinde As, Cd, Cs, Hg, Li, Pb, Se elementlerine rastlanmamış olup diğer elementler ve ağır metaller ortalama; Al 14,10 ±12,68 ppb, Ca 157,69±42,40 ppb, Cr 2,51±0,58 ppb, Cu 0,98±0,38 ppb, Fe 28,84±12,92 ppb, K 3920,12±1806,12 ppb, Mg 128,66± 33,08 ppb, Mn 3,93±2,61 ppb, Na 138,98±61,21 ppb, Ni 2,02±0,65 ppb ve Zn 9,71±6,74 ppb olarak tespit edilmiştir. -
Discovery and Description of the Bacterial Associates of a Gregarious Riparian Beetle with Explosive Defensive Chemistry
Discovery and Description of the Bacterial Associates of a Gregarious Riparian Beetle with Explosive Defensive Chemistry Item Type text; Electronic Thesis Authors McManus, Reilly Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 27/09/2021 16:02:09 Link to Item http://hdl.handle.net/10150/625915 DISCOVERY AND DESCRIPTION OF THE BACTERIAL ASSOCIATES OF A GREGARIOUS RIPARIAN BEETLE WITH EXPLOSIVE DEFENSIVE CHEMISTRY by Reilly McManus _____________________________________________ Copyright © Reilly McManus 2017 A Thesis Submitted to the Faculty of the THE GRADUATE INTERDISCIPLINARY PROGRAM IN ENTOMOLOGY & INSECT SCIENCES In Partial Fulfillment of the Requirements For the Degree of MASTER OF SCIENCE In the Graduate College THE UNIVERSITY OF ARIZONA 2017 STATEMENT BY AUTHOR The thesis titled Discovery and Description of the Bacterial Associates of a Gregarious Riparian Beetle with Explosive Defensive Chemistry prepared by Reilly McManus has been submitted in partial fulfillment of requirements for a master’s degree at the University of Arizona and is deposited in the University Library to be made available to borroWers under rules of the Library. Brief quotations from this thesis are alloWable Without special permission, provided that an accurate acknoWledgement of the source is made. Requests for permission for extended quotation from or reproduction of this manuscript in Whole or in part may be granted by the head of the major department or the Dean of the Graduate College When in his or her judgment the proposed use of the material is in the interests of scholarship. -
Abstract Tracing Hydrocarbon
ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants. -
How Is the Gut Microbiota Affected?
microorganisms Article Honeybees Exposure to Natural Feed Additives: How Is the Gut Microbiota Affected? Daniele Alberoni † , Loredana Baffoni * , Chiara Braglia † , Francesca Gaggìa and Diana Di Gioia Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy; [email protected] (D.A.); [email protected] (C.B.); [email protected] (F.G.); [email protected] (D.D.G.) * Correspondence: [email protected]; Tel.: +39-051-2096-269 † These authors contributed equally to this work. Abstract: The role of a balanced gut microbiota to maintain health and prevent diseases is largely established in humans and livestock. Conversely, in honeybees, studies on gut microbiota pertur- bations by external factors have started only recently. Natural methods alternative to chemical products to preserve honeybee health have been proposed, but their effect on the gut microbiota has not been examined in detail. This study aims to investigate the effect of the administration of a bacterial mixture of bifidobacteria and Lactobacillaceae and a commercial product HiveAliveTM on honeybee gut microbiota. The study was developed in 18 hives of about 2500 bees, with six replicates for each experimental condition for a total of three experimental groups. The absolute abundance of main microbial taxa was studied using qPCR and NGS. The results showed that the majority of the administered strains were detected in the gut. On the whole, great perturbations upon the administration of the bacterial mixture and the plant-based commercial product were not observed in the gut microbiota. Significant variations with respect to the untreated control were only observed TM Citation: Alberoni, D.; Baffoni, L.; for Snodgrassella sp.