Automated Identification of Myxobacterial Genera Using Convolutional Neural Network
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The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
Emended Descriptions of the Genera Myxococcus and Corallococcus, Typification of the Species Myxococcus Stipitatus and Myxococcu
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 2122–2128 DOI 10.1099/ijs.0.003566-0 Emended descriptions of the genera Myxococcus and Corallococcus, typification of the species Myxococcus stipitatus and Myxococcus macrosporus and a proposal that they be represented by neotype strains. Request for an Opinion Elke Lang and Erko Stackebrandt Correspondence DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstr. Elke Lang 7B, 38124 Braunschweig Germany [email protected] The genus Corallococcus was separated from the genus Myxococcus mainly on the basis of differences in morphology and consistency of swarms and fruiting bodies of the respective members. Phylogenetic, chemotaxonomic and physiological evidence is presented here that underpins the separate status of these phylogenetically neighbouring genera. Emended descriptions of the two genera are presented. The data also suggest that the species Corallococcus macrosporus belongs to the genus Myxococcus. To the best of our knowledge, the type strains of the species Myxococcus macrosporus and Myxococcus stipitatus are not available from any established culture collection or any other source. A Request for an Opinion is made regarding the proposal that strain Cc m8 (5DSM 14697 5CIP 109128) be formally recognized as the neotype strain for the species Myxococcus macrosporus, replacing the designated type strain Windsor M271T, and that strain Mx s8 (5DSM 14675 5JCM 12634) be formally recognized as the neotype strain for the species Myxococcus stipitatus, replacing the designated type strain Windsor M78T. Introduction The genus Myxococcus was described by Thaxter (1892), Within the family Myxococcaceae, delineation of genera, who first recognized that the myxobacteria, formerly descriptions of species and affiliations of strains to species assigned to the fungi, were in fact bacteria. -
J. Gen. Appl. Microbiol., 48, 109–115 (2002)
J. Gen. Appl. Microbiol., 48, 109–115 (2002) Full Paper Haliangium ochraceum gen. nov., sp. nov. and Haliangium tepidum sp. nov.: Novel moderately halophilic myxobacteria isolated from coastal saline environments Ryosuke Fudou,* Yasuko Jojima, Takashi Iizuka, and Shigeru Yamanaka† Central Research Laboratories, Ajinomoto Co., Inc., Kawasaki 210–8681, Japan (Received November 21, 2001; Accepted January 31, 2002) Phenotypic and phylogenetic studies were performed on two myxobacterial strains, SMP-2 and SMP-10, isolated from coastal regions. The two strains are morphologically similar, in that both produce yellow fruiting bodies, comprising several sessile sporangioles in dense packs. They are differentiated from known terrestrial myxobacteria on the basis of salt requirements (2–3% NaCl) and the presence of anteiso-branched fatty acids. Comparative 16S rRNA gene sequencing studies revealed that SMP-2 and SMP-10 are genetically related, and constitute a new cluster within the myxobacteria group, together with the Polyangium vitellinum Pl vt1 strain as the clos- est neighbor. The sequence similarity between the two strains is 95.6%. Based on phenotypic and phylogenetic evidence, it is proposed that these two strains be assigned to a new genus, JCM؍) .Haliangium gen. nov., with SMP-2 designated as Haliangium ochraceum sp. nov .(DSM 14436T؍JCM 11304T؍) .DSM 14365T), and SMP-10 as Haliangium tepidum sp. nov؍11303T Key Words——Haliangium gen. nov.; Haliangium ochraceum sp. nov.; Haliangium tepidum sp. nov.; marine myxobacteria Introduction terized as Gram-negative, rod-shaped gliding bacteria with high GϩC content. Analyses of 16S rRNA gene Myxobacteria are unique in their complex life cycle. sequences reveal that they form a relatively homoge- Under starvation conditions, bacterial cells gather to- neous cluster within the d-subclass of Proteobacteria gether to form aggregates that subsequently differenti- (Shimkets and Woese, 1992). -
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 -
Marine Myxobacteria As a Source of Antibiotics—Comparison of Physiology, Polyketide-Type Genes and Antibiotic Production of Three New Isolates of Enhygromyxa Salina
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Mar. Drugs 2010, 8, 2466-2479; doi:10.3390/md8092466 OPEN ACCESS Marine Drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Marine Myxobacteria as a Source of Antibiotics—Comparison of Physiology, Polyketide-Type Genes and Antibiotic Production of Three New Isolates of Enhygromyxa salina Till F. Schäberle 1, Emilie Goralski 1, Edith Neu 1, Özlem Erol 1, Georg Hölzl 2, Peter Dörmann 2, Gabriele Bierbaum 3 and Gabriele M. König 1,* 1 Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany; E-Mails: [email protected] (T.F.S.); [email protected] (E.G.); [email protected] (E.N.); [email protected] (Ö.E.) 2 Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany; E-Mails: [email protected] (G.H.); [email protected] (P.D.) 3 Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany; E-Mail: [email protected] (G.B.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +49-228-733747; Fax: +49-228-733250. Received: 12 August 2010; in revised form: 25 August 2010 / Accepted: 1 September 2010 / Published: 3 September 2010 Abstract: Three myxobacterial strains, designated SWB004, SWB005 and SWB006, were obtained from beach sand samples from the Pacific Ocean and the North Sea. -
Soil Bacterial and Fungal Communities of Six Bahiagrass Cultivars
Soil bacterial and fungal communities of six bahiagrass cultivars Lukas Beule1,2, Ko-Hsuan Chen2, Chih-Ming Hsu2, Cheryl Mackowiak2, Jose C.B. Dubeux Jr.3, Ann Blount2 and Hui-Ling Liao2 1 Molecular Phytopathology and Mycotoxin Research, Georg-August Universität Göttingen, Goettingen, Germany 2 North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America 3 North Florida Research and Education Center, University of Florida, Marianna, FL, United States of America ABSTRACT Background. Cultivars of bahiagrass (Paspalum notatum Flüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as microbiome taxa have repeatedly been shown to be directly linked to plant performance. Objectives. This study aimed to determine whether different bahiagrass cultivars interactively influence soil bacterial and fungal communities. Methods. Six bahiagrass cultivars (`Argentine', `Pensacola', `Sand Mountain', `Tifton 9', `TifQuik', and `UF-Riata') were grown in a randomized complete block design with four replicate plots of 4.6 × 1.8 m per cultivar in a Rhodic Kandiudults soil in Northwest Florida, USA. Three soil subsamples per replicate plot were randomly collected. Soil DNA was extracted and bacterial 16S ribosomal RNA and fungal ribosomal internal transcribed spacer 1 genes were amplified and sequenced with one Illumina Miseq Nano. Results. The soil bacterial and fungal community across bahiagrass cultivars showed similarities with communities recovered from other grassland ecosystems. Few dif- ferences in community composition and diversity of soil bacteria among cultivars were detected; none were detected for soil fungi. -
Activated Sludge Microbial Community and Treatment Performance of Wastewater Treatment Plants in Industrial and Municipal Zones
International Journal of Environmental Research and Public Health Article Activated Sludge Microbial Community and Treatment Performance of Wastewater Treatment Plants in Industrial and Municipal Zones Yongkui Yang 1,2 , Longfei Wang 1, Feng Xiang 1, Lin Zhao 1,2 and Zhi Qiao 1,2,* 1 School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; [email protected] (Y.Y.); [email protected] (L.W.); [email protected] (F.X.); [email protected] (L.Z.) 2 China-Singapore Joint Center for Sustainable Water Management, Tianjin University, Tianjin 300350, China * Correspondence: [email protected]; Tel.: +86-22-87402072 Received: 14 November 2019; Accepted: 7 January 2020; Published: 9 January 2020 Abstract: Controlling wastewater pollution from centralized industrial zones is important for reducing overall water pollution. Microbial community structure and diversity can adversely affect wastewater treatment plant (WWTP) performance and stability. Therefore, we studied microbial structure, diversity, and metabolic functions in WWTPs that treat industrial or municipal wastewater. Sludge microbial community diversity and richness were the lowest for the industrial WWTPs, indicating that industrial influents inhibited bacterial growth. The sludge of industrial WWTP had low Nitrospira populations, indicating that influent composition affected nitrification and denitrification. The sludge of industrial WWTPs had high metabolic functions associated with xenobiotic and amino acid metabolism. Furthermore, bacterial richness was positively correlated with conventional pollutants (e.g., carbon, nitrogen, and phosphorus), but negatively correlated with total dissolved solids. This study was expected to provide a more comprehensive understanding of activated sludge microbial communities in full-scale industrial and municipal WWTPs. Keywords: activated sludge; industrial zone; metabolic function; microbial community; wastewater treatment 1. -
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b r a z i l i a n j o u r n a l o f m i c r o b i o l o g y 4 9 (2 0 1 8) 248–257 ht tp://www.bjmicrobiol.com.br/ Environmental Microbiology Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota Muhammad Yasir King Abdulaziz University, King Fahd Medical Research Center, Special Infectious Agents Unit, Jeddah, Saudi Arabia a r a t b i c l e i n f o s t r a c t Article history: In this study for the first-time microbial communities in the caves located in the mountain Received 12 October 2016 range of Hindu Kush were evaluated. The samples were analyzed using culture-independent Accepted 15 August 2017 (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon Available online 18 October 2017 sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Acti- Associate Editor: John McCulloch nobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Keywords: Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis Caves of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the stud- 16S ribosomal RNA ied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Microbiota Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Antimicrobial Thirty strains among the identified isolates from both caves showed antimicrobial activ- Sediments ity. -
Novel Myxobacteria As a Potential Source of Natural Products and Description of Inter-Species Nature of C-Signal
Novel myxobacteria as a potential source of natural products and description of inter-species nature of C-signal Dissertation zur Erlangung des Grades des Doktors der Naturwissenschaften der Naturwissenschaftlich-Technischen Fakultät III Chemie, Pharmazie, Bio- und Werkstoffwissenschaften der Universität des Saarlandes von Ram Prasad Awal (M. Sc. in Medical Microbiology) Saarbrücken 2016 Tag des Kolloquiums: ......19.12.2016....................................... Dekan: ......Prof. Dr. Guido Kickelbick.............. Berichterstatter: ......Prof. Dr. Rolf Müller...................... ......Prof. Dr. Manfred J. Schmitt........... ............................................................... Vositz: ......Prof. Dr. Uli Kazmaier..................... Akad. Mitarbeiter: ......Dr. Jessica Stolzenberger.................. iii Diese Arbeit entstand unter der Anleitung von Prof. Dr. Rolf Müller in der Fachrichtung 8.2, Pharmazeutische Biotechnologie der Naturwissenschaftlich-Technischen Fakultät III der Universität des Saarlandes von Oktober 2012 bis September 2016. iv Acknowledgement Above all, I would like to express my special appreciation and thanks to my advisor Professor Dr. Rolf Müller. It has been an honor to be his Ph.D. student and work in his esteemed laboratory. I appreciate for his supervision, inspiration and for allowing me to grow as a research scientist. Your guidance on both research as well as on my career have been invaluable. I would also like to thank Professor Dr. Manfred J. Schmitt for his scientific support and suggestions to my research work. I am thankful for my funding sources that made my Ph.D. work possible. I was funded by Deutscher Akademischer Austauschdienst (DAAD) for 3 and half years and later on by Helmholtz-Institute. Many thanks to my co-advisors: Dr. Carsten Volz, who supported and guided me through the challenging research and Dr. Ronald Garcia for introducing me to the wonderful world of myxobacteria. -
Dissimilatory Nitrate Reduction to Ammonium in the Yellow River
www.nature.com/scientificreports OPEN Dissimilatory Nitrate Reduction to Ammonium in the Yellow River Estuary: Rates, Abundance, and Received: 13 April 2017 Accepted: 13 June 2017 Community Diversity Published online: 28 July 2017 Cuina Bu, Yu Wang, Chenghao Ge, Hafz Adeel Ahmad, Baoyu Gao & Shou-Qing Ni Dissimilatory nitrate reduction to ammonium (DNRA) is an important nitrate reduction process in estuarine sediments. This study reports the frst investigation of DNRA in the Yellow River Estuary located in Eastern Shandong, China. Saltwater intrusion could afect the physicochemical characteristics and change the microbial community structure of sediments. In this study, the activity, abundance and community diversity of DNRA bacteria were investigated during saltwater intrusion. The slurry incubation experiments combined with isotope-tracing techniques and qPCR results showed that DNRA rates and nrfA (the functional gene of DNRA bacteria) gene abundance varied over wide ranges across diferent sites. DNRA rates had a positive and signifcant correlation with sediment + organic content and extractable NH4 , while DNRA rates were weakly correlated with nrfA gene abundance. In comparison, the activities and abundance of DNRA bacteria did not change with a trend along salinity gradient. Pyrosequencing analysis of nrfA gene indicated that delta-proteobacteria was the most abundant at all sites, while epsilon-proteobacteria was hardly found. This study reveals that variability in the activities and community structure of DNRA bacteria is largely driven by changes in environmental factors and provides new insights into the characteristics of DNRA communities in estuarine ecosystems. Rapid economic development and human activities are the major source of nutrients such as nitrogen which, when released into rivers, can cause the problem of eutrophication. -
Aberystwyth University Comparative Genomics and Pan-Genomics of the Myxococcaceae, Including a Description of Five Novel Species
Aberystwyth University Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species Chambers, James; Sparks, Natalie; Sydney, Natashia; Livingstone, Paul; Cookson, Alan; Whitworth, David Published in: Genome Biology and Evolution DOI: 10.1093/gbe/evaa212 Publication date: 2020 Citation for published version (APA): Chambers, J., Sparks, N., Sydney, N., Livingstone, P., Cookson, A., & Whitworth, D. (2020). Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov. Genome Biology and Evolution, 12(12), 2289-2302. https://doi.org/10.1093/gbe/evaa212 Document License CC BY-NC General rights Copyright and moral rights for the publications made accessible in the Aberystwyth Research Portal (the Institutional Repository) are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the Aberystwyth Research Portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the Aberystwyth Research Portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. tel: +44 1970 62 2400 email: [email protected] Download date: 01. -
The Soil Microbial Food Web Revisited: Predatory Myxobacteria As Keystone Taxa?
The ISME Journal https://doi.org/10.1038/s41396-021-00958-2 ARTICLE The soil microbial food web revisited: Predatory myxobacteria as keystone taxa? 1 1 1,2 1 1 Sebastian Petters ● Verena Groß ● Andrea Söllinger ● Michelle Pichler ● Anne Reinhard ● 1 1 Mia Maria Bengtsson ● Tim Urich Received: 4 October 2018 / Revised: 24 February 2021 / Accepted: 4 March 2021 © The Author(s) 2021. This article is published with open access Abstract Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5–9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized fi 1234567890();,: 1234567890();,: predatory bacteria af liated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition.