DOCSLIB.ORG

COALITION Ingrid Groth1, Cesareo Saiz- Jimenez2

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
COALITION Ingrid Groth1, Cesareo Saiz- Jimenez2 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC COALITION No. 4, March 2002 Moore, D.M. (1992). Lichen Flora of Within the frame of EC project ENVA- Great Britain and Ireland. 710 pp. Natural CT95-0104 microbial colonization in both History Museum, London. caves Was studied by conventional isolation and cultivation techniques. Wirth, V. (1995). Die Flechten Baden- Sampling Was done by touching the rock Württembergs Teil 1 & 2. Ulmer, between the paintings With sterile cotton Stuttgart. [Superb colour photographs, swabs and suspending the adherent keys, notes on ecology, etc.; in German.] bacteria in sterile 0.15 sodium phosphate buffer solution. Additionally contact Macrophotographs on line plates With different culture media and http://dbiodbs.uniV.trieste.it/web/lich/arch_icon pieces of rock or soil material Were used http://www.lias.net/index.cfm for isolation of microorganisms from different sites in the caves. Ecology Nimis, P.L. (1993). The Lichens of Italy. Pure cultures of actinomycete isolates An annotated catalogue. Museo were classified by morphological, Regionale di Scienze Naturali. selected physiological and Monographie XII. Torino. pp. 897. chemotaxonomic methods. On the basis of a polyphasic taxonomic approach in Purvis, O.W., Coppins, B.J., most of the cases a tentatiVe genus Hawksworth, D.L., James, P.W. and affiliation was possible. Moore, D.M. (1992) Lichen Flora of Great Britain and Ireland. 710 pp. Natural As the result of our study it Was stated History Museum, London. that actinomycetes Were the most abundant microorganisms in the two Glossary caves (Groth et al. 1999, 1999a, 2001). Hawksworth, D.L., Kirk, P.M., Sutton, The term actinomycetes refers to all B.C. and Pegler, D.N. (1995) Ainsworth Gram-positiVe bacteria With a high G+C & Bisby's Dictionary of the Fungi. Eighth content (> 55 mol %) in their DNA. Edition, XII + 616 pp. International Actinomycetes are morphologically Mycological Institute. CAB International. diverse and comprise different mophological types; irregular rods, cocci and filamentous or mycelium forming ACTINOMYCETES IN CAVES organisms. Ingrid Groth1, Cesareo Saiz- The cave isolates could be affiliated to 2 11 different families of the order Jimenez Actinomycetales, class Actinobacteria. 1 Hans-Knöll-Institute for Natural Products This fact indicates a high phylogenetic Research, Jena, Germany. diversity Which has been deVeloped 2 Instituto de Recursos Naturales y within these special biotopes (Table 1). Agrobiologia, Sevilla, Spain. Furthermore it Was demonstrated by fatty acid profiles (MIDI system), Parietal paintings are Valuable Works of utilization patterns of 95 different carbon art giving evidence of prehistoric life. In sources (BIOLOG-System) combined With many cases these paintings were morphological studies that there was an detected by chance after thousands of equally high diversity at the species or years as it happened upon the Altamira strain leVels Within the isolates being Cave in Spain and the Grotta dei Cervi in affilated to genera. Italy. While the Altamira CaVe (discovered in 1879) had been opened to The predominant actinomycete isolates tourists reaching a daily flow of up to from both caves belong to the genus 3000 visitors in the 1970's, the access Streptomyces. Members of this genus to the Grotta dei CerVi (discovered in are known for their Versatile metabolic 1970) has been restricted only to activities. In dependence on scientists. environmental or cultural conditions in the laboratory actinomycetes are able to 12 COALITION No. 4, March 2002 produce a Wealth of structural diverse Our studies in the two different caves chemical compounds including pigments reVealed that mass growth of and organic acids Which may contribute actinomycetes seemed to be controlled in to biodeterioration of Works of art. an undisturbed environment, like Grotta dei CerVi, by natural factors (low temperature, high humidity and limited Table 1: Taxonomic diversity of actinomycetes from the Altamira Cave and Grotta dei Cervi amount of nutrients). While microbial Family Genus colonization in the Grotta dei CerVi did Brevibacteriaceae Brevibacterium not result in Visible damages of the Dermabacteraceae Brachybacterium paintings over thousands of years, the Gordoniaceae Gordonia deteriorations obserVed in the caves of Microbacteriaceae Agromyces Altamira and Lascaux after their opening Microbacterium Micrococcaceae Arthrobacter clearly demonstrate the negative effects Micrococcus of mass tourism Within a relative short Rothia period. Micromonosporaceae Micromonospora Nocardiaceae Nocardia Rhodococcus To combine both access to works of art Nocardioidaceae Nocardioides in underground environments and to Nocardiopsaceae Nocardiopsis preserVe these early manifestations of Pseudonocardiaceae Amycolatopsis prehistoric life, basic multidisciplinary Saccharothrix studies are necessary. Concerning Streptomycetaceae Streptomyces microbial colonization both noncultural (Rölleke et al. 1996) and cultural techniques should be combined. While Furthermore Cañaveras et al. (1999) molecular approaches based on detection suggested that actinomycetes may play a and identification of DNA sequences role in the formation of moonmilk encoding for 16S rRNA or 23S rRNA deposits in hypersaline environments of equally include culturable and some caves as actinomycetes (mainly nonculturable bacteria, classical isolation streptomycetes) Were isolated from and cultivation techniques selectively hydromagnesite and needle fiber support the growth of only a minor aragonite deposits in the Altamira CaVe. fraction of the really existing bacteria in a This assumption was supported by the special biotope. HoweVer pure cultures of fact that numerous actinomycete isolates selected bacteria obtained by isolation were able to produce either calcite or procedures enable scientists to study the both calcite and Vaterite crystals under metabolic actiVities of these organisms special laboratory conditions (Groth et al. and contribute to a better understanding 2001). of their role in biodecay processes. Furthermore living cultures are a It is noW generally accepted that prerequisite for the discovery and biodeterioration of outdoor monuments is description of novel taxa from these not only caused by phototrophic interesting but up to now less studied microorganisms and fungi coVering the environments. The occurrence of novel surfaces With green or dark biofilms but bacteria Was confirmed by recent is rather a concerted action of diverse publications of two novel genera isolated procaryotic and eucaryotic from a Chinese caVe (Groth et al. 1999, microorganisms. Among the 2002). heterotrophic bacteria actinomycetes predominate in hypogean environments. References They are able to colonize nearly all CañaVeras J.C., Hoyos M., Sanchez-Moral S., Sanz-Rubio habitats and can adapt to Very poor and E., Bedoya J., Soler V., Groth I., Schumann P., Laiz L., Gonzalez I., Saiz-Jimenez C. (1999). Microbial highly saline environments, e.g. communities associated With hydromagnesite and stalactites. By formation of dormant cells needle-fiber aragonite deposits in a karstic caVe actinomycetes can surVive unfavourable (Altamira, Northern Spain). Geomicrobiol. J. 16, 9-25. Groth I., Saiz-Jimenez J. (1999). Actinomycetes in conditions. hypogean environments. Geomicrobiol. J. 16, 1-8. Groth I., Vettermann R., Schuetze B., Schumann P., Saiz- Jimenez C. (1999a). Actinomycetes in karstic caVes of 13 COALITION No. 4, March 2002 Northern Spain (Altamira and Tito Bustillo). J. Preliminary programme Microbiol. Meth. 36, 115-122. Groth I., Schumann P., Schuetze B., AuGsten K., Kramer I., Stackebrandt E. (1999b). Beutenbergia cavernae gen. November 8th nov., sp. nov., an L-lysine-containinG actinomycete isolated from a cave. Int. J. Syst. Bacteriol. 49, 1733- Session 1. Biodeterioration Processes: 1740. organic/inorganic substrates Groth I., Schumann P., Laiz L., Sanchez-Moral S., Session 2. Diagnostic techniques Cañaveras J. C. (2001). GeomicrobioloGical study of the Grotta dei Cervi, Porto Badisco, Italy. (traditional and innovative) Geomicrobiol. J. 18, 241-258. Session 3. Intervention procedures: Groth I., Schumann P., Schuetze B., AuGsten K., Stackebrandt E. (2002). Knoellia sinensis gen. nov., chemical (biocides) - Pysical/mechanical sp. nov. and Knoellia subterranea sp. nov., two novel (laser, UV) actinobacteria isolated from a cave. Int. J. Syst. Evol. Microbiol. 52, 77-84. Session 4. Bioremediation Rölleke S., Muyzer G., Wawer C., Wanner G., Lubitz W. (1996). Identification of bacteria in a biodeGraded wall November 9th paintinG by denaturinG Gradient Gel electrophoresis of PCR-amplified Gene fraGments codinG for 16S rRNA. Session 5. Biohazard in Restoration: Appl. Environ. Microbiol. 62, 2059-2065. AllerGenic and pathoGenic, toxicity. Session 6. Health protection guidelines Session 7. COALITION questionnaire. Forthcoming activities Send your preliminary inscription form (to be distributed) to [email protected] QUESTIONNAIRE ON THE APPLICATION OF MOLECULAR BIOLOGICAL TECHNIQUES IN CONSERVATION INTERNATIONAL CONFERENCE ON A questionnaire is beinG prepared by MOLECULAR BIOLOGY AND CULTURAL Caroline Kyi on behalf of COALITION to HERITAGE know the real impact on molecular tools into the conservation field and its An International Conference on Molecular feasibility in microbiological assessment. Biology and Cultural Heritage will be This will be distributed in April to the organized
Load more

Recommended publications
  • 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.
    [Show full text]
  • Kaistella Soli Sp. Nov., Isolated from Oil-Contaminated Soil
    A001 Kaistella soli sp. nov., Isolated from Oil-contaminated Soil Dhiraj Kumar Chaudhary1, Ram Hari Dahal2, Dong-Uk Kim3, and Yongseok Hong1* 1Department of Environmental Engineering, Korea University Sejong Campus, 2Department of Microbiology, School of Medicine, Kyungpook National University, 3Department of Biological Science, College of Science and Engineering, Sangji University A light yellow-colored, rod-shaped bacterial strain DKR-2T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10–35°C, at pH 6.0– 9.0, and at 0–1.5% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-2T was affiliated to the genus Kaistella, with the closest species being Kaistella haifensis H38T (97.6% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine as the principal polar lipids;iso-C15:0, antiso-C15:0, and summed feature 9 (iso-C17:1 9c and/or C16:0 10-methyl) as the main fatty acids; and menaquinone-6 as a major menaquinone. The DNA G + C content was 39.5%. In addition, the average nucleotide identity (ANIu) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain DKR-2T and phylogenically closest members were below the threshold values for species delineation. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-2T represents a novel species in the genus Kaistella, for which the name Kaistella soli sp. nov. is proposed with the type strain DKR-2T (= KACC 22070T = NBRC 114725T). [This study was supported by Creative Challenge Research Foundation Support Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF- 2020R1I1A1A01071920).] A002 Chitinibacter bivalviorum sp.
    [Show full text]
  • Seed Interior Microbiome of Rice Genotypes Indigenous to Three
    Raj et al. BMC Genomics (2019) 20:924 https://doi.org/10.1186/s12864-019-6334-5 RESEARCH ARTICLE Open Access Seed interior microbiome of rice genotypes indigenous to three agroecosystems of Indo-Burma biodiversity hotspot Garima Raj1*, Mohammad Shadab1, Sujata Deka1, Manashi Das1, Jilmil Baruah1, Rupjyoti Bharali2 and Narayan C. Talukdar1* Abstract Background: Seeds of plants are a confirmation of their next generation and come associated with a unique microbia community. Vertical transmission of this microbiota signifies the importance of these organisms for a healthy seedling and thus a healthier next generation for both symbionts. Seed endophytic bacterial community composition is guided by plant genotype and many environmental factors. In north-east India, within a narrow geographical region, several indigenous rice genotypes are cultivated across broad agroecosystems having standing water in fields ranging from 0-2 m during their peak growth stage. Here we tried to trap the effect of rice genotypes and agroecosystems where they are cultivated on the rice seed microbiota. We used culturable and metagenomics approaches to explore the seed endophytic bacterial diversity of seven rice genotypes (8 replicate hills) grown across three agroecosystems. Results: From seven growth media, 16 different species of culturable EB were isolated. A predictive metabolic pathway analysis of the EB showed the presence of many plant growth promoting traits such as siroheme synthesis, nitrate reduction, phosphate acquisition, etc. Vitamin B12 biosynthesis restricted to bacteria and archaea; pathways were also detected in the EB of two landraces. Analysis of 522,134 filtered metagenomic sequencing reads obtained from seed samples (n=56) gave 4061 OTUs.
    [Show full text]
  • Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 1 Microalgae 2 Richard G. Do
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. 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 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley,
    [Show full text]
  • The Bacterial Communities of Sand-Like Surface Soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Yang Wang
    The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Yang Wang To cite this version: Yang Wang. The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA). Agricultural sciences. Université Paris-Saclay, 2015. English. NNT : 2015SACLS120. tel-01261518 HAL Id: tel-01261518 https://tel.archives-ouvertes.fr/tel-01261518 Submitted on 25 Jan 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. NNT : 2015SACLS120 THESE DE DOCTORAT DE L’UNIVERSITE PARIS-SACLAY, préparée à l’Université Paris-Sud ÉCOLE DOCTORALE N°577 Structure et Dynamique des Systèmes Vivants Spécialité de doctorat : Sciences de la Vie et de la Santé Par Mme Yang WANG The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Thèse présentée et soutenue à Orsay, le 23 Novembre 2015 Composition du Jury : Mme. Marie-Claire Lett , Professeure, Université Strasbourg, Rapporteur Mme. Corinne Cassier-Chauvat , Directeur de Recherche, CEA, Rapporteur M. Armel Guyonvarch, Professeur, Université Paris-Sud, Président du Jury M.
    [Show full text]
  • And Diacylglycerol Lipase from Marine Member Janibacter Sp
    Int. J. Mol. Sci. 2014, 15, 10554-10566; doi:10.3390/ijms150610554 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article Biochemical Properties of a New Cold-Active Mono- and Diacylglycerol Lipase from Marine Member Janibacter sp. Strain HTCC2649 Dongjuan Yuan 1, Dongming Lan 1, Ruipu Xin 1, Bo Yang 2 and Yonghua Wang 1,* 1 College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China; E-Mails: [email protected] (D.Y.); [email protected] (D.L.); [email protected] (R.X.) 2 School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel./Fax: +86-20-8711-3842. Received: 29 April 2014 / in revised form: 15 May 2014 / Accepted: 22 May 2014 / Published: 12 June 2014 Abstract: Mono- and di-acylglycerol lipase has been applied to industrial usage in oil modification for its special substrate selectivity. Until now, the reported mono- and di-acylglycerol lipases from microorganism are limited, and there is no report on the mono- and di-acylglycerol lipase from bacteria. A predicted lipase (named MAJ1) from marine Janibacter sp. strain HTCC2649 was purified and biochemical characterized. MAJ1 was clustered in the family I.7 of esterase/lipase. The optimum activity of the purified MAJ1 occurred at pH 7.0 and 30 °C. The enzyme retained 50% of the optimum activity at 5 °C, indicating that MAJ1 is a cold-active lipase.
    [Show full text]
  • Bioinformatic and Mutational Studies of Related Toxin–Antitoxin Pairs in M
    Bioinformatic and mutational studies of related toxin–antitoxin pairs in M. tuberculosis predict and identify key functional residues Running title: Toxin-Antitoxin relationships in M.tuberculosis Himani Tandon1, Arun Sharma2, Saruchi Wadhwa2, Raghavan Varadarajan1, Ramandeep Singh2, Narayanaswamy Srinivasan1*, and Sankaran Sandhya1* 1Molecular Biophysics Unit, Indian Institute of Science, Bangalore- 560012, India. 2Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, PO Box # 4, Faridabad, Haryana- 121001, India. * To whom correspondence should be addressed. Sankaran Sandhya: Molecular Biophysics Unit, Indian Institute of Science, Bangalore- 560012; [email protected]; Tel: +918022932837; Fax: +918023600535. Correspondence may also be addressed to Narayanaswamy Srinivasan. Molecular Biophysics Unit, Indian Institute of Science, Bangalore- 560012; [email protected]; Tel: +918022932837; Fax: +918023600535. Keywords: Toxin-antitoxin, homology, paralogues, structure-function, Mycobacterium tuberculosis, genome analysis, bacteriostasis, VapBC, PIN domain, phylogeny, molecular modelling, protein evolution 1 S1. Trends observed in the distribution of homologues of M.tuberculosis TA systems within MTBC and conservation pattern of Rv0909-Rv0910 and Rv1546 in MTBC and other organisms. Ramage et. al, have earlier probed the spread of M.tuberculosis type II TA in 5 of the 10 genomes in the MTBC complex (1). In addition to these genomes, we have included the genomes of M.orygis, M.caprae and M.mungi that are now available since their study, for our analysis. A search of M.tuberculosis TA in MTBC revealed that not all TAs were found as a pair with the same confidence in M.mungi, M.orygis and M.canetti.
    [Show full text]
  • International Journal of Speleology International Journal of Speleology
    International Journal of Speleology 38 (1) 11-22 Bologna (Italy) January 2009 Available online at www.ijs.speleo.it International Journal of Speleology Official Journal of Union Internationale de Spéléologie Ultraviolet Radiation Sensitivity in Cave Bacteria: Evidence of Adaptation to the Subsurface? Jessica R. Snider1, Caitlin Goin2, Robert V. Miller2, Penelope J. Boston3,4 and Diana E. Northup5 Abstract: Snider J.R., Goin C., Miller R.V., Boston P.J. and Northup D.E. 2009. Ultraviolet Radiation Sensitivity in Cave Bacteria: Evidence of Adaptation to the Subsurface? International Journal of Speleology, 38 (1), 13-22. Bologna (Italy). ISSN 0392-6672. We hypothesize that a reduced capacity to withstand or repair cellular damage from ultraviolet radiation may be present in cave- adapted microorganisms that never experience such conditions. However, a small number of previous studies have shown that some subsurface bacteria do not show greater sensitivity to ultraviolet radiation (UVR) than surface bacteria. To estimate UVR sensitivity in cave bacteria, bacterial isolates were collected from Carlsbad Cavern, New Mexico, U.S.A., and percent survival following exposure to various UVC and UVA radiation doses was determined. Cave bacteria from Left Hand Tunnel in Carlsbad Cavern and surface bacteria from soil and rocks above Carlsbad Cavern were grown on low and high nutrient media then exposed to 0, 10,000 and 20,000 μWs/ cm2 of UVR in a laboratory biological safety cabinet. Incubations were conducted at 15°C or 37ºC, in accordance with the isolates’ natural temperature environments. In addition, DNA repair capacity was estimated by exposing the organisms to various doses of UVC radiation and measuring survivability.
    [Show full text]
  • Plant-Derived Benzoxazinoids Act As Antibiotics and Shape Bacterial Communities
    Supplemental Material for: Plant-derived benzoxazinoids act as antibiotics and shape bacterial communities Niklas Schandry, Katharina Jandrasits, Ruben Garrido-Oter, Claude Becker Contents Supplemental Tables 2 Supplemental Table 1. Phylogenetic signal lambda . .2 Supplemental Table 2. Syncom strains . .3 Supplemental Table 3. PERMANOVA . .6 Supplemental Table 4. PERMANOVA comparing only two treatments . .7 Supplemental Table 5. ANOVA: Observed taxa . .8 Supplemental Table 6. Observed diversity means and pairwise comparisons . .9 Supplemental Table 7. ANOVA: Shannon Diversity . 11 Supplemental Table 8. Shannon diversity means and pairwise comparisons . 12 Supplemental Table 9. Correlation between change in relative abundance and change in growth . 14 Figures 15 Supplemental Figure 1 . 15 Supplemental Figure 2 . 16 Supplemental Figure 3 . 17 Supplemental Figure 4 . 18 1 Supplemental Tables Supplemental Table 1. Phylogenetic signal lambda Class Order Family lambda p.value All - All All All All 0.763 0.0004 * * Gram Negative - Proteobacteria All All All 0.817 0.0017 * * Alpha All All 0 0.9998 Alpha Rhizobiales All 0 1.0000 Alpha Rhizobiales Phyllobacteriacae 0 1.0000 Alpha Rhizobiales Rhizobiacaea 0.275 0.8837 Beta All All 1.034 0.0036 * * Beta Burkholderiales All 0.147 0.6171 Beta Burkholderiales Comamonadaceae 0 1.0000 Gamma All All 1 0.0000 * * Gamma Xanthomonadales All 1 0.0001 * * Gram Positive - Actinobacteria Actinomycetia Actinomycetales All 0 1.0000 Actinomycetia Actinomycetales Intrasporangiaceae 0.98 0.2730 Actinomycetia Actinomycetales Microbacteriaceae 1.054 0.3751 Actinomycetia Actinomycetales Nocardioidaceae 0 1.0000 Actinomycetia All All 0 1.0000 Gram Positive - All All All All 0.421 0.0325 * Gram Positive - Firmicutes Bacilli All All 0 1.0000 2 Supplemental Table 2.
    [Show full text]
  • View and Research Objectives
    University of Alberta Carotenoid diversity in novel Hymenobacter strains isolated from Victoria Upper Glacier, Antarctica, and implications for the evolution of microbial carotenoid biosynthesis by Jonathan Lee Klassen A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology and Cell Biotechnology Department of Biological Sciences ©Jonathan Lee Klassen Fall 2009 Edmonton, Alberta Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission. Examining Committee Dr. Julia Foght, Department of Biological Science Dr. Phillip Fedorak, Department of Biological Sciences Dr. Brenda Leskiw, Department of Biological Sciences Dr. David Bressler, Department of Agriculture, Food and Nutritional Science Dr. Jeffrey Lawrence, Department of Biological Sciences, University of Pittsburgh Abstract Many diverse microbes have been detected in or isolated from glaciers, including novel taxa exhibiting previously unrecognized physiological properties with significant biotechnological potential. Of 29 unique phylotypes isolated from Victoria Upper Glacier, Antarctica (VUG), 12 were related to the poorly studied bacterial genus Hymenobacter including several only distantly related to previously described taxa.
    [Show full text]
  • Metagenomic Analyses of Bacteria on Human Hairs: a Qualitative Assessment for Applications in Forensic Science Tridico Et Al
    Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science Tridico et al. Tridico et al. Investigative Genetics 2014, 5:16 http://www.investigativegenetics.com/content/5/1/16 Tridico et al. Investigative Genetics 2014, 5:16 http://www.investigativegenetics.com/content/5/1/16 RESEARCH Open Access Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science Silvana R Tridico1,2*, Dáithí C Murray1,2, Jayne Addison1, Kenneth P Kirkbride3 and Michael Bunce1,2 Abstract Background: Mammalian hairs are one of the most ubiquitous types of trace evidence collected in the course of forensic investigations. However, hairs that are naturally shed or that lack roots are problematic substrates for DNA profiling; these hair types often contain insufficient nuclear DNA to yield short tandem repeat (STR) profiles. Whilst there have been a number of initial investigations evaluating the value of metagenomics analyses for forensic applications (e.g. examination of computer keyboards), there have been no metagenomic evaluations of human hairs—a substrate commonly encountered during forensic practice. This present study attempts to address this forensic capability gap, by conducting a qualitative assessment into the applicability of metagenomic analyses of human scalp and pubic hair. Results: Forty-two DNA extracts obtained from human scalp and pubic hairs generated a total of 79,766 reads, yielding 39,814 reads post control and abundance filtering. The results revealed the presence of unique combinations of microbial taxa that can enable discrimination between individuals and signature taxa indigenous to female pubic hairs. Microbial data from a single co-habiting couple added an extra dimension to the study by suggesting that metagenomic analyses might be of evidentiary value in sexual assault cases when other associative evidence is not present.
    [Show full text]
  • Knoellia Sinensis Gen. Nov., Sp. Nov. and Knoellia Subterranea Sp. Nov., Two Novel Actinobacteria Isolated from a Cave
    International Journal of Systematic and Evolutionary Microbiology (2002), 52, 77–84 Printed in Great Britain Knoellia sinensis gen. nov., sp. nov. and Knoellia subterranea sp. nov., two novel actinobacteria isolated from a cave 1 Hans-Kno$ ll-Institut fu$ r Ingrid Groth,1 Peter Schumann,2 Barbara Schu$ tze,1 Kurt Augsten3 Naturstoff-Forschung e.V., 2 D-07745 Jena, Germany and Erko Stackebrandt 2 DSMZ–Deutsche Sammlung von Mikroorganismen und Author for correspondence: Ingrid Groth. Tel: j49 36 41 65 66 66. Fax: j49 36 41 65 66 60. Zellkulturen GmbH, e-mail: igroth!pmail.hki-jena.de D-38124 Braunschweig, Germany 3 Institut fu$ r Molekulare Two novel strains of the class Actinobacteria were isolated from a cave in Biotechnologie e.V., China. Cells of both strains were Gram-positive, non-motile, non-spore-forming D-07745 Jena, Germany and not acid-fast and exhibited a rod/coccus growth cycle. Both isolates grew well on complex organic media under aerobic conditions. Their cell wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The acyl type of the glycan chain of peptidoglycan was acetyl. The major respiratory quinone was MK-8(H4). The cellular fatty acid profile was characterized by the predominance of 13-methyltetradecanoic (i-C15:0), 15-methylhexadecanoic (i-C17:0), 14-methylpentadecanoic (i-C16:0) and 14-methylhexadecanoic (ai-C17:0) acids. The major polar lipids were phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. Mycolic acids were absent. The DNA GMC composition was 68–69 mol%. 16S rDNA-based phylogenetic analysis revealed an intermediate phylogenetic position of the cave isolates between the genera Janibacter and Tetrasphaera, which did not permit their unambiguous affiliation to either genus.
    [Show full text]