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Airborne Bacterial and Eukaryotic Community Structure Across the United Kingdom Revealed by High-Throughput Sequencing

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Supplementary Airborne Bacterial and Eukaryotic Community Structure Across the United Kingdom Revealed by High-Throughput Sequencing Hokyung Song, Ian Crawford, Jonathan R. Lloyd *, Clare H. Robinson, Christopher Boothman, Keith Bower, Martin Gallagher *, Grant Allen and David Topping Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, UK; [email protected] (H.S.); [email protected] (I.C.); [email protected] (C.H.R.); [email protected] (C.B.); [email protected] (K.B.); [email protected] (G.A.); [email protected] (D.T.) * Correspondence: [email protected] (J.R.L.); [email protected] (M.G.) Supplementary Figures Figure S1. 96 hour HYSPLIT Lagrangian back trajectories of air sampled at: (a) Chilbolton at 950 m, (b) Chilbolton at 380 m, and (c) Weybourne at 724 m. Figure S2. Canonical correspondence analysis result plot. Each of CH10, CH20, CH30 indicates samples collected in Chilbolton at high elevation (range of 950-1000 m asl) in the time duration of 10 min, 20 min, and 30 min. Each of W10, W20, W30 indicates samples collected in Weybourne (height range of 650-1000 m) in the time duration of 10 min, 20 min, and 30 min. Figure S3. Number of bacterial OTUs. Each of CH10, CH20, CH30 indicates samples collected in Chilbolton at high elevation (range of 950-1000 m asl) in the time duration of 10 min, 20 min, and 30 min. Each of W10, W20, W30 indicates samples collected in Weybourne (height range of 650-1000 m) in the time duration of 10 min, 20 min, and 30 min. Figure S4. Redundancy analysis result plot. Each of CH10, CH30 indicates samples collected in Chilbolton at high elevation (range of 950-1000 m asl) in the Table 10. min and 30 min. Each of CL10, CL20, CL30 indicates samples collected in Chilbolton at low elevation (range of 300-450 m asl) in the time duration of 10 min, 20 min, and 30 min. Each of W10, W20, W30 indicates samples collected in Weybourne (height range of 650-1000 m) in the time duration of 10 min, 20 min, and 30 min. Figure S5. Number of Eukaryotic OTUs. Each of CH10, CH30 indicates samples collected in Chilbolton at high elevation (range of 950–1000 m asl) in the time duration of 10 min and 30 min. Each of CL10, CL20, CL30 indicates samples collected in Chilbolton at low elevation (range of 300–450 m asl) in the time duration of 10 min, 20 min, and 30 min. Each of W10, W20, W30 indicates samples collected in Weybourne (height range of 650–1000 m) in the time duration of 10 min, 20 min, and 30 min. Supplementary tables. Table S1. Detailed information of collected filter samples. “lat” stands for latitude, “lon” stands for longitude, and “alt” stands for altitude. Relative humidity was calculated using the Arden Buck equation (Buck 1981). Average Start End Start End Average Start End Relative Filter ID Run Location Latitude/Longitude Latitude/Longitude Altitude Altitude Temperature Time Time Humidity (°) (°) (km) (km) (℃) (%) leg 1 Chilbolton 11:26:30 11:37:40 50.7962/−2.6726 51.0184/−1.7314 0.436 0.354 12.995 48.508 Chilbolton low 30 min leg 2 Chilbolton 11:44:38 11:54:37 51.1384/−1.4495 50.8815/−2.3144 0.378 0.406 13.817 46.741 leg 3 Chilbolton 11:57:11 12:08:01 50.8672/−2.3676 51.1309/−1.4658 0.385 0.320 14.089 45.837 Chilbolton low 10 min leg 1 Chilbolton 11:26:30 11:37:40 50.7962/−2.6726 51.0184/−1.7314 0.436 0.354 12.995 48.508 leg 1 Chilbolton 11:44:38 11:54:37 51.1384/−1.4495 50.8815/−2.3144 0.378 0.406 13.817 46.741 Chilbolton low 20 min leg 2 Chilbolton 11:57:11 12:08:01 50.8672/−2.3676 51.1309/−1.4658 0.385 0.320 14.089 45.837 leg 1 Chilbolton 12:14:15 12:24:19 51.0898/−1.5581 50.8384/−2.4859 0.975 0.974 8.196 62.864 Chilbolton high 30 min leg 2 Chilbolton 12:28:47 12:39:36 50.7926/−2.3218 51.1414/−1.4436 0.979 0.976 8.374 61.906 leg 3 Chilbolton 12:44:10 12:54:06 51.1324/−1.4567 50.9039/−2.3721 0.981 0.963 8.620 60.722 Chilbolton high 10 min leg 1 Chilbolton 12:14:15 12:24:19 51.0898/−1.5581 50.8384/−2.4859 0.975 0.974 8.196 62.864 leg 1 Chilbolton 12:28:47 12:39:36 50.7926/−2.3218 51.1414/−1.4436 0.979 0.976 8.374 61.906 Chilbolton high 20 min leg 2 Chilbolton 12:44:10 12:54:06 51.1324/−1.4567 50.9039/−2.3721 0.981 0.963 8.620 60.722 leg 1 Weybourne 13:36:05 13:46:18 52.9406/0.55184 52.8147/1.5293 0.973 0.677 7.519 37.590 Weybourne 30 min leg 2 Weybourne 13:50:10 13:59:16 52.8763/1.3028 52.9563/0.36313 0.670 0.673 8.515 56.670 leg 3 Weybourne 14:02:10 14:13:10 52.9452/0.4676 52.8768/1.5355 0.679 0.670 8.181 55.923 Weybourne 10 min leg 1 Weybourne 13:36:05 13:46:18 52.9406/0.55184 52.8147/1.5293 0.973 0.677 7.519 37.590 leg 1 Weybourne 13:50:10 13:59:16 52.8763/1.3028 52.9563/0.36313 0.670 0.673 8.515 56.670 Weybourne 20 min leg 2 Weybourne 14:02:10 14:30:10 52.9452/0.4676 53.1219/0.8797 0.679 2.593 7.596 56.309 Table S2. Blast result of the 20 most abundant bacterial OTUs. Among 100 best hits, only the hit results with highest similarity, highest score, and lowest e-value are shown. If there are multiple best hit sequences with the same similarity, e-value, and hit score, they are shown together. OTU ID Genus (Silva Database) Blast (NCBI NT Database) Similarity E−value Hit Score OTU008 Gordonia Gordonia iterans 100 1.96E-127 466 OTU009 Psychroglaciecola uncultured bacterium OTU010 Burkholderiaceae_unclassified Hydrogenophaga soli 99.206 4.24E-124 455 OTU011 Lautropia uncultured bacterium OTU013 Morganella Morganella morganii, Providencia rustigianii, Salmonella enterica, Escherichia coli 100 1.96E-127 466 OTU014 Candidatus_Udaeobacter uncultured bacterium OTU015 Fusobacterium Fusobacterium nucleatum 100 7.01E-127 464 Janibacter indicus, Janibacter hoylei, Janibacter terrae, Knoellia locipacati, Janibacter anophelis, OTU016 Intrasporangiaceae_unclassified Janibacter melonis, Janibacter limosus, Knoellia sinensis, Janibacter massiliensis, Knoellia 100 1.96E-127 466 subterranea OTU017 Chryseobacterium Chryseobacterium hominis 100 1.96E-127 466 OTU018 Sphingomonas uncultured bacterium OTU019 Pajaroellobacter uncultured bacterium Streptococcus oralis, Streptococcus mitis, Streptococcus infantis, Streptococcus pyogenes, OTU020 Streptococcus 100 7.01E-127 464 Streptococcus australis, Streptococcus sanguinis, Streptococcus pneumoniae OTU021 Nakamurella uncultured bacterium Arthrobacter davidanieli, Arthrobacter russicus, Psychromicrobium silvestre, Psychromicrobium OTU022 Micrococcaceae_unclassified 100 1.96E-127 466 lacuslunae OTU023 Actinomyces Actinomyces oris, Actinomyces naeslundii, Actinomyces viscosus 100 1.96E-127 466 OTU024 Rubellimicrobium uncultured bacterium Chryseobacterium bernardetii, Bergeyella porcorum, Chryseobacterium taichungense, OTU026 uncultured 95.635 4.33E-109 405 Chryseobacterium moechotypicola OTU028 Burkholderiaceae_unclassified Tepidimonas taiwanensis 99.6 1.18E-124 457 OTU029 Gemella Gemella haemolysans, Gemella morbillorum 100 1.96E-127 466 OTU030 Devosia uncultured bacterium Table S3. Blast result of the 20 most abundant eukaryotic OTUs. Among 100 best hits, only the hit results with highest similarity, highest score, and lowest e-value are shown. If there are multiple best hit sequences with the same similarity, e-value, and hit score, they are shown together. OTU ID Genus Blast Result Similarity E-value Hit Score OTU0002 Embryophyta unclassified Pinus luchuensis 100 4.81E-50 207 Cladosporium tenuissimum, Cladosporium halotolerans, Cladosporium xylophilum, Cladosporium oxysporum, Cladosporium exasperatum, Cladosporium herbarum, Panicum hallii, Cladosporium anthropophilum, Selaginella moellendorffii, Cladosporium xanthochromaticum, Cladosporium velox, Cladosporium tenellum, Cladosporium subinflatum, Cladosporium sphaerospermum, OTU0001 Cladosporium Cladosporium ramotenellum, Cladosporium pulvericola, Cladosporium pseudocladosporioides, 100 6.07E-49 204 Cladosporium perangustum, Cladosporium parasubtilissimum, Cladosporium parahalotolerans, Cladosporium neolangeronii, Cladosporium needhamense, Cladosporium lycoperdinum, Cladosporium limoniforme, Cladosporium langeronii, Cladosporium inversicolor, Cladosporium funiculosum, Cladosporium floccosum, Cladosporium dominicanum OTU0010 Phoma Epicoccum sorghinum (also known as Phoma sorghina), Epicoccum nigrum, Curvularia kusanoi 100 6.07E-49 204 OTU0012 Chlamydomonadal unclassified Chloromonas subdivisa 100 7.65E-48 200 Vigna unguiculata, Brassica oleracea, Brassica rapa, Eutrema salsugineum, Brassica carinata, Brassica napus, Brassica juncea, Raphanus sativus, Raphanus raphanistrum, Brassica oleracea, OTU0008 Brassicales unclassified 100 4.81E-50 207 Brassica nigra, Arabis alpina, Thlaspi arvense, Nasturtium officinale, Matthiola longipetala, Sisymbrium orientale, Isatis tinctoria, Draba nemorosa, Brassica tournefortii Moesziomyces antarcticus, Ustilago maydis, Sporisorium reilianum, Pseudozyma hubeiensis, OTU0009 Ustilaginaceae unclassified Melanopsichium pennsylvanicum, Ustilago williamsii, Ustilago striiformis, Ustilago cynodontis, 100 1.71E-49 206 Tranzscheliella hypodytes, Macalpinomyces bursus, Melanopsichium pennsylvanicum OTU0016 Pleosporales unclassified Torula herbarum 100 6.07E-49 204 OTU0027 Blumeria Blumeria graminis 99.091 2.82E-47 198 OTU0032 Pleosporales unclassified Phaeosphaeria graminis, Neocucurbitaria acanthocladae, Alternaria alternariae 100 6.07E-49 204 OTU0015 Hemiptera Aulacorthum solani 99.194 5.43E-55 224 OTU0014 Ranunculales unclassified Ranunculus japonicus 100 4.81E-50 207 OTU0029 Blumeria Blumeria graminis 100 6.07E-49 204 OTU0025 Sclerotinia
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    Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2006 Phylogeny of Hinterhubera, Novenia and related genera based on the nuclear ribosomal (nr) DNA sequence data (Asteraceae: Astereae) Vesna Karaman Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Karaman, Vesna, "Phylogeny of Hinterhubera, Novenia and related genera based on the nuclear ribosomal (nr) DNA sequence data (Asteraceae: Astereae)" (2006). LSU Doctoral Dissertations. 2200. https://digitalcommons.lsu.edu/gradschool_dissertations/2200 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. PHYLOGENY OF HINTERHUBERA, NOVENIA AND RELATED GENERA BASED ON THE NUCLEAR RIBOSOMAL (nr) DNA SEQUENCE DATA (ASTERACEAE: ASTEREAE) A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Vesna Karaman B.S., University of Kiril and Metodij, 1992 M.S., University of Belgrade, 1997 May 2006 "Treat the earth well: it was not given to you by your parents, it was loaned to you by your children. We do not inherit the Earth from our Ancestors, we borrow it from our Children." Ancient Indian Proverb ii ACKNOWLEDGMENTS I am indebted to many people who have contributed to the work of this dissertation.
  • Non-Commercial Use Only

    Non-Commercial Use Only

    Infectious Disease Reports 2019; volume 11:8132 Janibacter species with most reliable diagnostic tool. However, evidence of genomic sometimes a diagnosis cannot be made Correspondence: Ying Bai, Division of using blood culture because of poor labora- Vector-Borne Diseases, Centers for Disease polymorphism isolated tory infrastructure, presence of uncommon Control and Prevention, 3156 Rampart Road, from resected heart valve pathogens, or pretreatment of the patient Fort Collins, Colorado 80521 USA. in a patient with aortic stenosis with antibiotics prior to sample collection. Tel. 1-970-266-3555. Up to 35% of all infective endocarditis E-mail: [email protected] cases remain blood culture negative either Lile Malania,1 Ying Bai,2 Key words: aortic stenosis; bacteria; genome 3 4 due to slow growth of the bacteria or inap- polymorphism; Janibacter. Kamil Khanipov, Marika Tsereteli, 2 5 1 propriate media. Mikheil Metreveli, David Tsereteli, Calcific aortic stenosis is also a major 1 1 Acknowledgements: The authors would like Ketevan Sidamonidze, Paata Imnadze, problem in many countries. In the United to thank Natalia Abazashvili, Tamriko 3 2 Yuriy Fofanov, Michael Kosoy States, the incidence rate of aortic stenosis Giorgadze, and Nazibrola Chitadze for their 1National Center for Disease Control has been reported as 27.1 per 10,000.3 The assistance with laboratory tests; Guram and Public Health, Tbilisi, Georgia; mechanism of calcification remains unclear. Katstadze, and Neli Chakvetadze for their par- ticipation in investigation of the human case; 2Division of Vector-Borne Diseases, The hypothesis is that low grade chronic or recurrent bacterial endocarditis with specif- Levent Albayrak and George Golovko for the Centers for Disease Control and assistance with genome analysis; and ic calcifiable bacteria is a cause of calcifica- Prevention, Fort Collins, CO, USA; 4 Christina Nelson for careful revision of the 3Department of Pharmacology and tion of the aortic valves.
  • WO 2014/121298 A2 7 August 2014 (07.08.2014) P O P C T

    WO 2014/121298 A2 7 August 2014 (07.08.2014) P O P C T

    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2014/121298 A2 7 August 2014 (07.08.2014) P O P C T (51) International Patent Classification: VULIC, Marin; c/o Seres Health, Inc., 161 First Street, A61K 39/02 (2006.01) Suite 1A, Cambridge, MA 02142 (US). (21) International Application Number: (74) Agents: HUBL, Susan, T. et al; Fenwick & West LLP, PCT/US2014/014738 Silicon Valley Center, 801 California Street, Mountain View, CA 94041 (US). (22) International Filing Date: 4 February 2014 (04.02.2014) (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, English (25) Filing Language: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (26) Publication Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (30) Priority Data: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 61/760,584 4 February 2013 (04.02.2013) US KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/760,585 4 February 2013 (04.02.2013) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/760,574 4 February 2013 (04.02.2013) us OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 61/760,606 4 February 2013 (04.02.2013) us SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, 61/926,918 13 January 2014 (13.01.2014) us TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, (71) Applicant: SERES HEALTH, INC.
  • View Full Text-PDF

    View Full Text-PDF

    Int.J.Curr.Microbiol.App.Sci (2020) 9(4): 284-302 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 9 Number 4 (2020) Journal homepage: http://www.ijcmas.com Original Research Article https://doi.org/10.20546/ijcmas.2020.904.035 Optimization of Nutritional Variables Using Response Surface Methodology for Enhanced Antifungal Metabolite Production by Janibacter sp. RC18 from Turmeric Rhizosphere Ruth Chiamaka Osaro-Matthew*, Francis Sopuruchukwu Ire and Nnenna Frank-peterside Department of Microbiology University of Port Harcourt Choba, Nigeria *Corresponding author ABSTRACT Antifungal metabolites from rare actinomycetes have been found attractive for application due to its novelty, potency and environmental friendliness. K e yw or ds Optimization of process variables for enhanced production of antifungal metabolite in Janibacter sp. RC18 was carried out in this study. One factor at a Janibacter sp. time (OFAT) was used for preliminary optimization of fermentation variables RC18, Antifungal (time, temperature, initial pH, carbon and nitrogen sources). A three factor central metabolite , OFAT, composite design (CCD) and response surface methodology (RSM) were Central composite design; Response employed for optimization of the selected significant nutritional variable (starch, surface soybean meal) and CaCO3. The optimum antifungal metabolite production was methodology o obtained at day 7 incubation period inhibition, temperature 30 C, pH 8, starch as carbon source and soybean meal as nitrogen source. Response surface analysis Article Info revealed that the optimum value of the variables were 10.76 g/l of starch, 11.95 g/l Accepted: of soybean meal and 1.57 g/l of CaCO . Under this optimal condition antifungal 04 March 2020 3 Available Online: metabolite production was 23.7 ± 0.09 mm which increased by 22.33 % compared 10 April 2020 to OFAT optimized medium (18.4 ± 0.06 mm).