DOCSLIB.ORG

Pseudonocardia Nantongensis Sp. Nov., a Novel Endophytic Actinomycete Isolated from the Coastal Halophyte Tamarix Chinensis Lour

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Pseudonocardia Nantongensis Sp. Nov., a Novel Endophytic Actinomycete Isolated from the Coastal Halophyte Tamarix Chinensis Lour Antonie van Leeuwenhoek DOI 10.1007/s10482-012-9764-5 ORIGINAL PAPER Pseudonocardia nantongensis sp. nov., a novel endophytic actinomycete isolated from the coastal halophyte Tamarix chinensis Lour Ke Xing • Sheng Qin • Guang-Kai Bian • Yue-Ji Zhang • Wen-Di Zhang • Chuan-Chao Dai • Chang-Hong Liu • Wen-Jun Li • Ji-Hong Jiang Received: 5 April 2012 / Accepted: 13 June 2012 Ó Springer Science+Business Media B.V. 2012 Abstract A novel isolate, designated strain KLBMP Pseudonocardia, being most closely related to Pseud- 1282T was isolated from the surface-sterilized leaves of onocardia kongjuensis LM 157T (98.33 %), Pseudono- a coastal halophyte Tamarix chinensis Lour., collected cardia autotrophica IMSNU 20050T (97.77 %), from Nantong, Jiangsu Province, east of China. Phylo- Pseudonocardia endophytica YIM 56035T (97.63 %), genetic analysis based on 16S rRNA gene sequences Pseudonocardia ammonioxydans H9 T (97.62 %) and revealed that this strain belongs to the genus Pseudonocardia compacta IMSNU 20111T (97.56 %); similarity to other type strains of the genus Pseudono- cardia was\97.5 %. Chemotaxonomic data confirmed T Electronic supplementary material The online version the affiliation of strain KLBMP 1282 to the genus of this article (doi:10.1007/s10482-012-9764-5) contains Pseudonocardia. Strain KLBMP 1282T contained MK- supplementary material, which is available to authorized users. 8(H4) as the predominant ubiquinone and iso-C16:0 as K. Xing Á S. Qin (&) Á G.-K. Bian Á Y.-J. Zhang Á the major fatty acid. The polar lipids detected in strain T W.-D. Zhang Á J.-H. Jiang (&) KLBMP 1282 were diphosphatidylglycerol, phosphat- The Key Laboratory of Biotechnology for Medicinal Plant idylglycerol, phosphatidylcholine, phosphatidylmethyletha- of Jiangsu Province, School of Life Science, Jiangsu nolamine, phosphatidylethanolamine, phosphatidylinositol, Normal University, Xuzhou, Jiangsu 221116, People’s Republic of China phosphatidylinositol mannosides, one unknown phospho- e-mail: [email protected] lipid and four unknown glycolipids. The DNA G ? C T J.-H. Jiang content of strain KLBMP 1282 was 73.1 mol %. The e-mail: [email protected] results of DNA–DNA hybridizations and the phyloge- netic analysis, together with the phenotypic and C.-C. Dai biochemical tests, allowed the differentiation of strain College of Life Sciences, Nanjing Normal University, T Nanjing 210046, China KLBMP 1282 from strains of other recognized Pseudonocardia species. Therefore, strain KLBMP C.-H. Liu 1282T represents a novel species of the genus Pseud- College of Life Sciences, Nanjing University, onocardia, for which the name Pseudonocardia nan- Nanjing 210093, China tongensis sp. nov. is proposed. The type strain is T T T W.-J. Li KLBMP 1282 (=KCTC 29053 = NBRC 108677 ). The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation Keywords Pseudonocardia nantongensis sp. nov Á and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan Coastal halophyte Á Endophytic Á Polyphasic 650091, People’s Republic of China taxonomy 123 Antonie van Leeuwenhoek Introduction Materials and methods The genus Pseudonocardia was firstly proposed by Isolation and maintenance of organism Henssen (1957) to accommodate nocardioform acti- nomycetes that have a type IV cell wall (contain meso- Strain KLBMP 1282T was isolated from the healthy diaminopimelic acid, with arabinose and galactose as leaves of a coastal halophyte Tamarix chinensis Lour., characteristic sugars) and lack mycolic acids. Mem- collected from the city of Nantong, Jiangsu Province, bers of the genus Pseudonocardia are composed of east of China. The samples were treated and surface vegetative and aerial mycelium with spore chains sterilized according to the five-step sterilization pro- produced by acropetal budding or fragmentation. The cedure (Qin et al. 2008). The samples were then major menaquinone is MK-8(H4)orMK-9and aseptically crumbled into smaller fragments using a phospholipids are either type PII or PIII pattern. The commercial blender (Joyoung, XC-001) and plated on DNA G ? C content for members of this genus ranges the selective isolation medium agar (starch 5 g, from 68 to 79 mol % (Lee et al. 2001). The description glucose 5 g, casein 2 g, yeast 1 g, CaCO3 2 g, agar of the genus was later emended by McVeigh et al. 15 g, 1 L distilled water, pH 7.0). The plates were (1994), Warwick et al. (1994), Reichert et al. (1998), incubated at 28 °C for 2–8 weeks and colonies were Huang et al. (2002), Park et al. (2008). At the time of obtained and subcultured on yeast extract-malt extract writing, the genus Pseudonocardia encompasses more agar (ISP 2 medium) at 4 °C and as glycerol suspen- than 40 species with validly published names, origi- sion (20 %, v/v) at -20 and -80 °C. Strain KLBMP nating from various environments (http://www.bacter 1282T was deposited in the NITE Biological Resource io.cict.fr/p/pseudonocardia.html). Interestingly, many Center (NBRC) as strain NBRC 108677T and in the new species of the genus Pseudonocardia were iso- Korean Collection for Type Cultures (KCTC) as strain lated from surface sterilized plants recently, such as KCTC 29053T. Pseudonocardia oroxyli (Gu et al. 2006), Pseudono- cardia endophytica (Chen et al. 2009), Pseudonocar- Phenotypic characterization dia acaciae (Duangmal et al. 2009), Pseudonocardia tropica (Qin et al. 2010), Pseudonocardia adelaiden- Cultural characteristics were observed on ISP 2, sis (Kaewkla and Franco 2010), Pseudonocardia oatmeal (ISP 3), inorganic salts-starch (ISP 4), glyc- kunmingensis (Zhao et al. 2011a), Pseudonocardia erol-asparagine (ISP 5) (Shirling and Gottlieb 1966), eucalypti (Kaewkla and Franco 2011), Pseudonocar- as well as potato-dextrose (PDA), Czapek’s and dia sichuanensis (Qin et al. 2011), Pseudonocardia nutrient agars (Waksman, 1967) for 14 days at artemisiae (Zhao et al. 2011b), Pseudonocardia ban- 28 °C. The colony colour was determined with the naensis (Zhao et al. 2011c) and Pseudonocardia ISCC–NBS colour charts (Kelly 1964). Cell morphol- serianimatus (Zhao et al. 2011d), indicating its high ogy was observed using light microscopy (SA3300- diversity within higher plants. PL) and scanning electron microscopy (Hitachi; During a study of the diversity of culturable S-3400N) using 4 weeks old nutrient agar medium endophytic actinobacteria associated with coastal culture (growth at 28 °C). Physiological tests of halophytes in eastern of China, an actinomycete growth at different temperatures (4, 10, 15, 20, 28, strain, designated KLBMP 1282T was isolated. The 32, 37, 45, 50 and 55 °C) and NaCl concentrations strain exhibited the typical morphological character- (0–20 %, w/v) (at intervals of 1 %, 28 °C) were istics of the genus Pseudonocardia. Here, we report examined by growing the novel strain on ISP 2 basal on the taxonomic characterization and classification medium. Growth at various pH values (4.0–11.0) were of strain KLBMP 1282T and our present study examined as described by Xu et al. (2005) by growing confirmed that it was a representative of a novel the strain in ISP 2 broth basal medium. Carbon source species within the genus Pseudonocardia, for which utilization tests and other phenotypic characteristics the name Pseudonocardia nantongensis sp. nov. is were carried out according to Kurup and Schmitt proposed. (1973) and Gordon et al. (1974). Nitrogen source 123 Antonie van Leeuwenhoek utilization was assessed according to Williams et al. 1981) algorithms. The phylogenetic consensus trees (1989). The type strains P. kongjuensis LM 157T, P. were reconstructed using MEGA version 5 (Tamura autotrophica IMSNU 20050T, P. endophytica YIM et al. 2011) for the neighbour-joining, maximum- 56035T, P. ammonioxydans H9T and P. compacta parsimony and maximum-likelihood methods. Boot- IMSNU 20111T were tested together under the same strap analysis was performed with 1,000 replications. conditions. DNA–DNA hybridization was performed using the microplate hybridization method (Ezaki et al. 1989;He Chemotaxonomy et al. 2005) and photobiotin-labelled DNA from strain KLBMP 1282T and P. kongjuensis LM 157T. DNA– For most chemotaxonomic analyses, cell mass was DNA relatedness was calculated as the mean of obtained from ISP 2 broth medium after cultivation for triplicate measurements. 10 days (at logarithmic growth phase) at 28 °C (150 rev min-1). Amino acids and sugars of whole- Nucleotide sequence accession number cell hydrolysates were analyzed by TLC as described previously (Staneck and Roberts 1974). For fatty acid The 16S rRNA gene sequence of strain KLBMP 1282T analysis, strain KLBMP 1282T and the reference strain determined in this study has been deposited in P. kongjuensis LM 157T were grown in nutrient broth GenBank under the accession number JQ819252. for 7 days at 28 °C. Extraction of fatty acid methyl esters, washing of extracts and GC analysis were performed according to the standard procedures of the Results and discussion Microbial Identification System (MIDI; Microbial ID) (Sasser 1990) using the MIDI Sherlock Version 6. 1, Cells of strain KLBMP 1282T were Gram-positive and MIDI database TSBA6. Polar lipids were extracted aerobic. Morphological observation of the 4 weeks according to the procedures described by Minnikin old culture of strain KLBMP 1282T revealed that both et al. (1979) and separated by two-dimensional TLC. aerial and vegetative hyphae were abundant, well Menaquinones were extracted and purified as developed and fragmented. The mycelia displayed described by Collins et al. (1977) and analysed by long spore chains, containing rod-shaped and smooth- HPLC (Groth et al. 1997). The G ? C content of the surfaced spores on NA medium agar (Supplementary DNA was determined by the method of Mesbah et al. Fig. S1). Strain KLBMP 1282T showed good growth (1989). on NA and PDA media, moderate growth on ISP 2, ISP 3 and ISP 5 media, and poor growth on ISP 4 and Molecular analysis Czapek’s agar media. White aerial mycelia were produced on tested media. The substrate mycelium Genomic DNA preparation, PCR amplification and varies from yellowish/yellow to orange-yellow.
Load more

Recommended publications
  • Pseudonocardia Acaciae Sp. Nov., Isolated from Roots of Acacia Auriculiformis A
    Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth. Page 1 of 2 Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth. 123 Kannika Duangmal , Arinthip Thamchaipenet , Atsuko Matsumoto and 3 Yoko Takahashi - Author Affiliations 1Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand 2Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand 3Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan Correspondence Kannika Duangmal [email protected] or [email protected] Abstract A novel Gram-positive-staining actinomycete designated strain GMKU095T was isolated from surface-sterilized roots of Acacia auriculiformis A. Cunn. ex Benth. (earpod wattle). The organism produced branching mycelium. The spores were non-motile and had a spiny surface. Growth of strain GMKU095T occurred at 18– 42 °C, pH 5.0–8.0 and at NaCl concentrations up to 5 %. Whole-cell hydrolysates contained arabinose and galactose as major characteristic sugars. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The glycan moiety of the murein contained acetyl residues. The menaquinone was MK-8(H4); mycolic acids were not detected. The G+C content of the DNA was 71.6 mol%. iso- C16 : 0 was detected as the major cellular fatty acid. Comparative studies of 16S rRNA gene sequences indicated that the strain was phylogenetically related to members of the genus Pseudonocardia. The most closely related type strain is Pseudonocardia spinosispora IMSNU 50581T , which is 96.2 % similar in 16S rRNA gene sequence.
    [Show full text]
  • Pseudonocardia Pini Sp. Nov., an Endophytic Actinobacterium Isolated from Roots of the Pine Tree Callitris Preissii
    Pseudonocardia Pini Sp. Nov., An Endophytic Actinobacterium Isolated From Roots of the Pine Tree Callitris Preissii Onuma Kaewkla ( [email protected] ) Mahasarakham University https://orcid.org/0000-0001-7630-7074 Christopher Milton Mathew Franco Flinders University of South Australia: Flinders University Research Article Keywords: Pseudonocardia pini sp. nov., an endophytic actinobacterium Posted Date: March 16th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-274242/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Archives of Microbiology on April 23rd, 2021. See the published version at https://doi.org/10.1007/s00203-021-02309-3. Page 1/16 Abstract A Gram positive, aerobic, actinobacterial strain with rod-shaped spores, CAP47RT, which was isolated from the surface-sterilized root of a native pine tree (Callitris preissii), South Australia is described. The major cellular fatty acid of this strain was iso-H-C16:1 and major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was identied as meso- diaminopimelic acid. These chemotaxonomic data conrmed the aliation of strain CAP47RT to the genus Pseudonocardia. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the family Pseudonocardiaceae, being most closely related to Pseudonocardia xishanensis JCM 17906T (98.8%), Pseudonocardia oroxyli DSM 44984T (98.7%), Pseudonocardia thailandensis CMU-NKS-70T (98.7%), and Pseudonocardia ailaonensis DSM 44979T (97.9%). The results of the polyphasic study which contain genome comparisons of ANIb, ANIm and digital DNA-DNA hybridization revealed the differentiation of strain CAP47RT from the closest species with validated names.
    [Show full text]
  • Successful Drug Discovery Informed by Actinobacterial Systematics
    Successful Drug Discovery Informed by Actinobacterial Systematics Verrucosispora HPLC-DAD analysis of culture filtrate Structures of Abyssomicins Biological activity T DAD1, 7.382 (196 mAU,Up2) of 002-0101.D V. maris AB-18-032 mAU CH3 CH3 T extract H3C H3C Antibacterial activity (MIC): S. leeuwenhoekii C34 maris AB-18-032 175 mAU DAD1 A, Sig=210,10 150 C DAD1 B, Sig=230,10 O O DAD1 C, Sig=260,20 125 7 7 500 Rt 7.4 min DAD1 D, Sig=280,20 O O O O Growth inhibition of Gram-positive bacteria DAD1 , Sig=310,20 100 Abyssomicins DAD1 F, Sig=360,40 C 75 DAD1 G, Sig=435,40 Staphylococcus aureus (MRSA) 4 µg/ml DAD1 H, Sig=500,40 50 400 O O 25 O O Staphylococcus aureus (iVRSA) 13 µg/ml 0 CH CH3 300 400 500 nm 3 DAD1, 7.446 (300 mAU,Dn1) of 002-0101.D 300 mAU Mode of action: C HO atrop-C HO 250 atrop-C CH3 CH3 CH3 CH3 200 H C H C H C inhibitior of pABA biosynthesis 200 Rt 7.5 min H3C 3 3 3 Proximicin A Proximicin 150 HO O HO O O O O O O O O O A 100 O covalent binding to Cys263 of PabB 100 N 50 O O HO O O Sea of Japan B O O N O O (4-amino-4-deoxychorismate synthase) by 0 CH CH3 CH3 CH3 3 300 400 500 nm HO HO HO HO Michael addition -289 m 0 B D G H 2 4 6 8 10 12 14 16 min Newcastle Michael Goodfellow, School of Biology, University Newcastle University, Newcastle upon Tyne Atacama Desert In This Talk I will Consider: • Actinobacteria as a key group in the search for new therapeutic drugs.
    [Show full text]
  • Production, Purification, and Characterization of Bioactive Metabolites Produced from Rare Actinobacteria Pseudonocardia Alni
    Online - 2455-3891 Vol 9, Suppl. 3, 2016 Print - 0974-2441 Research Article PRODUCTION, PURIFICATION, AND CHARACTERIZATION OF BIOACTIVE METABOLITES PRODUCED FROM RARE ACTINOBACTERIA PSEUDONOCARDIA ALNI RABAB OMRAN1*, MOHAMMED FADHIL KADHEM2 1Department of Biology, College of Science, University of Babylon, Babel, Al-Hillah, Iraq. 2Department of Pharmacology, Ibn Hayyan College, Karbala, Iraq. Email: [email protected], [email protected] Received: 30 August 2016, Revised and Accepted: 12 September 2016 ABSTRACT Objectives: Pseudonocardia alni exhibits antimicrobial activity against tested pathogenic Staphylococcus aureus, Microsporum canis, and Trichophyton mentagrophyte. The present paper aimed to optimize various cultural conditions for antimicrobial metabolite production, purification, and characterization of the active substance. Methods: The effects of various parameters such as culture media, carbon and nitrogen sources, phosphate concentration, pH, temperature, incubation period, and agitation rate on bioactive metabolite production were studied using a flask scale with varying single parameter. The active substances were purified by adsorption chromatography using Silica gel column and Sephadex LH 20 column, and the physical, chemical, and biological properties were characterized. Results: The metabolite production by P. alni was greatly influenced by various cultural conditions. It produced high levels of the antimicrobial substance in International Streptomyces project-2 broth compared with that in potato dextrose broth. The optimum parameters for antimicrobial production from the actinobacterium occurred in the production medium consisting of glucose (1%) and tryptone (1%), 0.001 M of K2HPO4 and the bioactive production. The purified active substance had relative factor Rf=0.53 in the mobile phase of a thin layer chromatography system and 0.05M glycine at initial pH 8.5 and incubated at 30°C for 4 d in stand incubator.
    [Show full text]
  • Genomic and Phylogenomic Insights Into the Family Streptomycetaceae Lead
    1 Supplementary Material 2 Genomic and phylogenomic insights into the family Streptomycetaceae lead 3 to proposal of Charcoactinosporaceae fam. nov. and 8 novel genera with 4 emended descriptions of Streptomyces calvus 5 Munusamy Madhaiyan1, †, *, Venkatakrishnan Sivaraj Saravanan2, †, Wah-Seng See-Too3, † 6 1Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 7 Singapore 117604; 2Department of Microbiology, Indira Gandhi College of Arts and Science, 8 Kathirkamam 605009, Pondicherry, India; 3Division of Genetics and Molecular Biology, 9 Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 10 Malaysia 1 11 Table S3. List of the core genes in the genome used for phylogenomic analysis. NCBI Protein Accession Gene WP_074993204.1 NUDIX hydrolase WP_070028582.1 YggS family pyridoxal phosphate-dependent enzyme WP_074992763.1 ParB/RepB/Spo0J family partition protein WP_070022023.1 lipoyl(octanoyl) transferase LipB WP_070025151.1 FABP family protein WP_070027039.1 heat-inducible transcriptional repressor HrcA WP_074992865.1 folate-binding protein YgfZ WP_074992658.1 recombination protein RecR WP_074991826.1 HIT domain-containing protein WP_070024163.1 adenylosuccinate synthase WP_009190566.1 anti-sigma regulatory factor WP_071828679.1 preprotein translocase subunit SecG WP_070026304.1 50S ribosomal protein L13 WP_009190144.1 30S ribosomal protein S5 WP_014674378.1 30S ribosomal protein S8 WP_070026314.1 50S ribosomal protein L5 WP_009300593.1 30S ribosomal protein S13 WP_003998809.1
    [Show full text]
  • Generalized Antifungal Activity and 454-Screening of Pseudonocardia and Amycolatopsis Bacteria in Nests of Fungus-Growing Ants
    Generalized antifungal activity and 454-screening SEE COMMENTARY of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants Ruchira Sena,1, Heather D. Ishaka, Dora Estradaa, Scot E. Dowdb, Eunki Honga, and Ulrich G. Muellera,1 aSection of Integrative Biology, University of Texas, Austin, TX 78712; and bMedical Biofilm Research Institute, 4321 Marsha Sharp Freeway, Lubbock, TX 79407 Edited by Raghavendra Gadagkar, Indian Institute of Science, Bangalore, India, and approved August 14, 2009 (received for review May 1, 2009) In many host-microbe mutualisms, hosts use beneficial metabolites origin (12–14). Many of the ant-associated Pseudonocardia species supplied by microbial symbionts. Fungus-growing (attine) ants are show antibiotic activity in vitro against Escovopsis (13–15). A thought to form such a mutualism with Pseudonocardia bacteria to diversity of actinomycete bacteria including Pseudonocardia also derive antibiotics that specifically suppress the coevolving pathogen occur in the ant gardens, in the soil surrounding attine nests, and Escovopsis, which infects the ants’ fungal gardens and reduces possibly in the substrate used by the ants for fungiculture (16, 17). growth. Here we test 4 key assumptions of this Pseudonocardia- The prevailing view of attine actinomycete-Escovopsis antago- Escovopsis coevolution model. Culture-dependent and culture- nism is a coevolutionary arms race between antibiotic-producing independent (tag-encoded 454-pyrosequencing) surveys reveal that Pseudonocardia and Escovopsis parasites (5, 18–22). Attine ants are several Pseudonocardia species and occasionally Amycolatopsis (a thought to use their integumental actinomycetes to specifically close relative of Pseudonocardia) co-occur on workers from a single combat Escovopsis parasites, which fail to evolve effective resistance nest, contradicting the assumption of a single pseudonocardiaceous against Pseudonocardia because of some unknown disadvantage strain per nest.
    [Show full text]
  • Pseudonocardia Parietis Sp. Nov., from the Indoor Environment
    This is an author manuscript that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology, copyright Society for General Microbiology, but has not been copy-edited, formatted or proofed. Cite this article as appearing in International Journal of Systematic and Evolutionary Microbiology. This version of the manuscript may not be duplicated or reproduced, other than for personal use or within the rule of ‘Fair Use of Copyrighted Materials’ (section 17, Title 17, US Code), without permission from the copyright owner, Society for General Microbiology. The Society for General Microbiology disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final copy-edited, published article, which is the version of record, can be found at http://ijs.sgmjournals.org, and is freely available without a subscription 24 months after publication. First published in: Int J Syst Evol Microbiol, 2009. 59(10) 2449-52. doi:10.1099/ijs.0.009993-0 Pseudonocardia parietis sp. nov., from the indoor environment J. Scha¨fer,1 H.-J. Busse2 and P. Ka¨mpfer1 Correspondence 1Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, D-35392 Giessen, P. Ka¨mpfer Germany [email protected] 2Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, giessen.de Austria A Gram-positive, rod-shaped, non-endospore-forming, mycelium-forming actinobacterium (04- St-002T) was isolated from the wall of an indoor environment colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 04-St-002T was shown to belong to the family Pseudonocardiaceae, and to be most closely related to Pseudonocardia antarctica (99.2 %) and Pseudonocardia alni (99.1 %).
    [Show full text]
  • Induction of Secondary Metabolism Across Actinobacterial Genera
    Induction of secondary metabolism across actinobacterial genera A thesis submitted for the award Doctor of Philosophy at Flinders University of South Australia Rio Risandiansyah Department of Medical Biotechnology Faculty of Medicine, Nursing and Health Sciences Flinders University 2016 TABLE OF CONTENTS TABLE OF CONTENTS ............................................................................................ ii TABLE OF FIGURES ............................................................................................. viii LIST OF TABLES .................................................................................................... xii SUMMARY ......................................................................................................... xiii DECLARATION ...................................................................................................... xv ACKNOWLEDGEMENTS ...................................................................................... xvi Chapter 1. Literature review ................................................................................. 1 1.1 Actinobacteria as a source of novel bioactive compounds ......................... 1 1.1.1 Natural product discovery from actinobacteria .................................... 1 1.1.2 The need for new antibiotics ............................................................... 3 1.1.3 Secondary metabolite biosynthetic pathways in actinobacteria ........... 4 1.1.4 Streptomyces genetic potential: cryptic/silent genes ..........................
    [Show full text]
  • Transition from Unclassified Ktedonobacterales to Actinobacteria During Amorphous Silica Precipitation in a Quartzite Cave Envir
    www.nature.com/scientificreports OPEN Transition from unclassifed Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment D. Ghezzi1,2, F. Sauro3,4,5, A. Columbu3, C. Carbone6, P.‑Y. Hong7, F. Vergara4,5, J. De Waele3 & M. Cappelletti1* The orthoquartzite Imawarì Yeuta cave hosts exceptional silica speleothems and represents a unique model system to study the geomicrobiology associated to silica amorphization processes under aphotic and stable physical–chemical conditions. In this study, three consecutive evolution steps in the formation of a peculiar blackish coralloid silica speleothem were studied using a combination of morphological, mineralogical/elemental and microbiological analyses. Microbial communities were characterized using Illumina sequencing of 16S rRNA gene and clone library analysis of carbon monoxide dehydrogenase (coxL) and hydrogenase (hypD) genes involved in atmospheric trace gases utilization. The frst stage of the silica amorphization process was dominated by members of a still undescribed microbial lineage belonging to the Ktedonobacterales order, probably involved in the pioneering colonization of quartzitic environments. Actinobacteria of the Pseudonocardiaceae and Acidothermaceae families dominated the intermediate amorphous silica speleothem and the fnal coralloid silica speleothem, respectively. The atmospheric trace gases oxidizers mostly corresponded to the main bacterial taxa present in each speleothem stage. These results provide novel understanding of the microbial community structure accompanying amorphization processes and of coxL and hypD gene expression possibly driving atmospheric trace gases metabolism in dark oligotrophic caves. Silicon is one of the most abundant elements in the Earth’s crust and can be broadly found in the form of silicates, aluminosilicates and silicon dioxide (e.g., quartz, amorphous silica).
    [Show full text]
  • Marine Rare Actinomycetes: a Promising Source of Structurally Diverse and Unique Novel Natural Products
    Review Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products Ramesh Subramani 1 and Detmer Sipkema 2,* 1 School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji; [email protected] 2 Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands * Correspondence: [email protected]; Tel.: +31-317-483113 Received: 7 March 2019; Accepted: 23 April 2019; Published: 26 April 2019 Abstract: Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
    [Show full text]
  • 1 Supplementary Material a Major Clade of Prokaryotes with Ancient
    Supplementary Material A major clade of prokaryotes with ancient adaptations to life on land Fabia U. Battistuzzi and S. Blair Hedges Data assembly and phylogenetic analyses Protein data set: Amino acid sequences of 25 protein-coding genes (“proteins”) were concatenated in an alignment of 18,586 amino acid sites and 283 species. These proteins included: 15 ribosomal proteins (RPL1, 2, 3, 5, 6, 11, 13, 16; RPS2, 3, 4, 5, 7, 9, 11), four genes (RNA polymerase alpha, beta, and gamma subunits, Transcription antitermination factor NusG) from the functional category of Transcription, three proteins (Elongation factor G, Elongation factor Tu, Translation initiation factor IF2) of the Translation, Ribosomal Structure and Biogenesis functional category, one protein (DNA polymerase III, beta subunit) of the DNA Replication, Recombination and repair category, one protein (Preprotein translocase SecY) of the Cell Motility and Secretion category, and one protein (O-sialoglycoprotein endopeptidase) of the Posttranslational Modification, Protein Turnover, Chaperones category, as annotated in the Cluster of Orthologous Groups (COG) (Tatusov et al. 2001). After removal of multiple strains of the same species, GBlocks 0.91b (Castresana 2000) was applied to each protein in the concatenation to delete poorly aligned sites (i.e., sites with gaps in more than 50% of the species and conserved in less than 50% of the species) with the following parameters: minimum number of sequences for a conserved position: 110, minimum number of sequences for a flank position: 110, maximum number of contiguous non-conserved positions: 32000, allowed gap positions: with half. The signal-to-noise ratio was determined by altering the “minimum length of a block” parameter.
    [Show full text]
  • Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 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 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain.
    [Show full text]