Phylogeographic Separation of Marine and Soil Myxobacteria at High Levels of Classification
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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. -
Two Independent Retrons with Highly Diverse Reverse Transcriptases In
Proc. Natl. Acad. Sci. USA Vol. 87, pp. 942-945, February 1990 Biochemistry Two independent retrons with highly diverse reverse transcriptases in Myxococcus xanthus (multicopy single-stranded DNA/2',5'-phosphodiester/codon usage/myxobacteria) SUMIKO INOUYE, PETER J. HERZER, AND MASAYORI INOUYE Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854 Communicated by Russell F. Doolittle, November 27, 1989 (received for review September 29, 1989) ABSTRACT A reverse transcriptase (RT) was recently found that the Mx65 retron is highly diverse and independent found in Myxococcus xanthus, a Gram-negative soil bacterium. from the Mx162 retron and that RT associated with the Mx65 This RT has been shown to be associated with a chromosomal retron has only 47% identity with RT for the Mx162 retron. region designated a retron responsible for the synthesis of a peculiar extrachromosomal DNA called msDNA (multicopy single-stranded DNA). We demonstrate that M. xanthus con- MATERIALS AND METHODS tains two independent, unlinked retrons, one for the synthesis Materials. The clone of the 9.0-kilobase (kb) Pst I fragment of msDNA-Mxl62 and the other for msDNA-Mx65. The struc- containing the Mx65 retron was obtained (8). Restriction tural analysis of the retron for msDNA-Mx65 revealed that the enzymes were purchased from New England Biolabs and coding regions for msdRNA (msr) and msDNA (msd), and an Boehringer Mannheim. open reading frame (ORF) downstream of msr are arranged in A deletion mutant strain ofthe Mx162 retron, AmsSX, was the same manner as found for the Mx162 retron. -
Isolation, Antimicrobial Activity of Myxobacterial Crude Extracts and Identification of the Most Potent Strains
Arch Biol Sci. 2017;69(3):561-568 https://doi.org/10.2298/ABS161011132C Isolation, antimicrobial activity of myxobacterial crude extracts and identification of the most potent strains Ivana Charousová*, Juraj Medo and Soňa Javoreková Department of Microbiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia *Corresponding author: [email protected] Received: October 11, 2016; Revised: November 14, 2016; Accepted: November 18, 2016; Published online: December 14, 2016 Abstract: Broad spectrum antimicrobial agents are urgently needed to fight frequently occurring multidrug-resistant pathogens. Myxobacteria have been regarded as “microbe factories” for active secondary metabolites, and therefore, this study was performed to isolate two bacteriolytic genera of myxobacteria, Myxococcus sp. and Corallococcus sp., from 10 soil/sand samples using two conventional methods followed by purification with the aim of determining the antimicrobial activity of methanol extracts against 11 test microorganisms (four Gram-positive, four Gram-negative, two yeasts and one fungus). Out of thirty-nine directly observed strains, 23 were purified and analyzed for antimicrobial activities. Based on the broth microdilution method, a total of 19 crude extracts showed antimicrobial activity. The range of inhibited wells was more important in the case of anti-Gram-positive-bacterial activity in comparison with the anti-Gram-negative-bacterial and antifungal activity. In light of the established degree and range of antimicrobial activity, two of the most active isolates (BNEM1 and SFEC2) were selected for further characterization. Morphological parameters and a sequence similarity search by BLAST revealed that they showed 99% sequence similarity to Myxococcus xanthus − BNEM1 (accession no. -
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). -
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. -
723874V1.Full.Pdf
bioRxiv preprint doi: https://doi.org/10.1101/723874; this version posted August 5, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Discovery of a polybrominated aromatic 2 secondary metabolite from a planctomycete 3 points at an ambivalent interaction with its 4 macroalgae host 5 6 7 8 9 10 11 Fabian Panter[a,b], Ronald Garcia[a,b], Angela Thewes[a,b], Nestor Zaburannyi [a,b], Boyke Bunk [b,c], Jörg 12 Overmann[b,c], Mary Victory Gutierrez [d], Daniel Krug[a,b] and Rolf Müller*[a,b] 13 14 15 * Corresponding author, rolf.mü[email protected] 16 17 18 19 20 [a] Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz 21 Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, 22 Germany 23 [b] German Centre for Infection Research (DZIF), Partner Site Hannover–Braunschweig, Germany 24 [c] Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 3814 Braunschweig, 25 Germany 26 [d] Biology Department, Far Eastern University, Nicanor Reyes St., Sampaloc, Manila, 1008 Metro Manila, Philippines 27 28 29 30 31 1 bioRxiv preprint doi: https://doi.org/10.1101/723874; this version posted August 5, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
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. -
Polyamine Distribution Profiles Among Some Members Within Delta-And Epsilon-Subclasses of Proteobacteria
Microbiol. Cult. Coll. June. 2004. p. 3 ― 8 Vol. 20, No. 1 Polyamine Distribution Profiles among Some Members within Delta-and Epsilon-Subclasses of Proteobacteria Koei Hamana1)*, Tomoko Saito1), Mami Okada1), and Masaru Niitsu2) 1)Department of Laboratory Sciences, School of Health Sciences, Faculty of Medicine, Gunma University, 39- 15 Showa-machi 3-chome, Maebashi, Gunma 371-8514, Japan 2)Faculty of Pharmaceutical Sciences, Josai University, Keyakidai 1-chome-1, Sakado, Saitama 350-0295, Japan Cellular polyamines of 18 species(13 genera)belonging to the delta and epsilon subclasses of the class Proteobacteria were analyzed by HPLC and GC. In the delta subclass, the four marine myxobacteria(the order Myxococcales), Enhygromyxa salina, Haliangium ochroceum, Haliangium tepidum and Plesiocystis pacifica contained spermidine. Fe(III)-reducing two Geobacter species and two Pelobacter species belonging to the order Desulfuromonadales con- tained spermidine. Bdellovibrio bacteriovorus was absent in cellular polyamines. Bacteriovorax starrii contained putrescine and spermidine. Bacteriovorax stolpii contained spermidine and homo- spermidine. Spermidine was the major polyamine in the sulfate-reducing delta proteobacteria belonging to the genera Desulfovibrio, Desulfacinum, Desulfobulbus, Desulfococcus and Desulfurella, and some species of them contained cadaverine. Within the epsilon subclass, three Sulfurospirillum species ubiquitously contained spermidine and one of the three contained sper- midine and cadaverine. Thiomicrospora denitrificans contained cadaverine and spermidine as the major polyamine. These data show that cellular polyamine profiles can be used as a chemotaxonomic marker within delta and epsilon subclasses. Key words: polyamine, spermidine, homospermidine, Proteobacteria The class Proteobacteria is a major taxon of the 18, 26). Fe(Ⅲ)-reducing members belonging to the gen- domain Bacteria and is phylogenetically divided into the era Pelobacter, Geobacter, Desulfuromonas and alpha, beta, gamma, delta and epsilon subclasses. -
Perspectives
Copvright 0 1999 bv the Genetics Society of Anlerica Perspectives Anecdotal, Historical and Critical Commentaries on Genetics Edited by James F. Crow and William F. Dove ROLANDTHAXTER’S Legacy and the Origins of Multicellular Development Dale Kaiser Departments of Biochemistry and of Developmental Biology, Stanford University, Stanford, Calijornia 94305 OLAND THAXTER published a bombshell in R December,1892. He reported that Chondro- myces crocatus, before then considered an imperfect fungus because of its complex fruiting bodv, was ac- tually a bacterium (Figure 1). THAXTERhad discov- ered theunicellular vegetative stage of C. crocatus; the cells he found were relatively short and they divided by binary fission. C. crocatus was, heconcluded, a “communal bacterium.” THAXTERdescribed the lo- comotion, swarming, aggregation and process of fruit- ing body formation of C. crocatus and its relatives, which are collectively called myxobacteria, with an accuracy that has survived 100 years of scrutiny. He recognized the behavioral similarity to the myxomv- cetes and the cellular slime molds, drawing attention in all three to the transition from single cells to an integrated multicellular state. He described the be- havior of myxobacteria in fructification in terms of a “course of development” because it was “a definitely recurring aggregation of individuals capable of con- certed action toward a definiteend” (THAXI‘ER1892). This essay will emphasize some implications of THAX- TER’S demonstrations, often apparently unrecognized. The striking similarities to cellular slime mold de- velopment probably led JOHN TYLERBONNER and KENNETHB. RAPER,50 years after THAXTER’Sdiscov- ery, to take independent forays into myxobacterial development. RAPER,an eminent mycologist, had in FIGURE1 .“Chondromyces crocatus fruiting bodv.