Volatile-Mediated Interactions in the Rhizosphere

Total Page:16

File Type:pdf, Size:1020Kb

Volatile-Mediated Interactions in the Rhizosphere Volatile-mediated interactions in the rhizosphere Viviane Cordovez da Cunha Thesis committee Promotors Prof. Dr F.P.M. Govers Personal Chair at the Laboratory of Phytopathology Wageningen University Prof. Dr J. M. Raaijmakers Professor of Microbial Ecology Leiden University Head of the Department of Microbial Ecology Netherlands Institute of Ecology, Wageningen Co-promotor Dr V. J. Carrion Researcher at the Department of Microbial Ecology Netherlands Institute of Ecology, Wageningen Other members Prof. Dr J.J.A. van Loon, Wageningen University Dr K. Vrieling, Leiden University Prof. Dr J.S. Dickschat, University of Bonn, Germany Prof. Dr L. Eberl, University of Zürich, Switzerland This research was conducted under the auspices of the Graduate School of Experimental Plant Sciences. Volatile-mediated interactions in the rhizosphere Viviane Cordovez da Cunha Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr A.P.J. Mol, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 4th November 2016 at 4 p.m. in the Aula. Viviane Cordovez da Cunha Volatile-mediated interactions in the rhizosphere, 220 pages. PhD thesis, Wageningen University, Wageningen, NL ( 2016) With references, with summaries in English, Dutch and Portuguese ISBN 978-94-6257-901-9 DOI: http://dx.doi.org/10.18174/388360 Table of Contents Chapter 1 General introduction and thesis outline 7 Chapter 2 Volatile affairs in microbial interactions 21 Chapter 3 Diversity and functions of volatile organic compounds 33 produced by Streptomyces from a disease-suppressive soil Chapter 4 Genomic and functional analyses of rhizospheric and 61 endophytic Microbacterium species Chapter 5 Exploring volatile organic compounds of Microbacterium 95 for plant growth promotion and biocontrol Chapter 6 Volatiles from a soil-borne pathogenic fungus modulate 111 the trade-off between plant growth and insect resistance Chapter 7 General discussion 155 References 167 Summary 187 Samenvatting 193 Resumo 199 Acknowledgments 205 About the author 211 Publications 211 Education statement 215 Chapter 1 General introduction and thesis outline CHAPTER ONE | 9 Volatile organic compounds (VOCs) are carbon containing molecules of low molecular weight and high vapor pressure that can easily evaporate and diffuse through soil and atmosphere. Due to these physical-chemical properties, they can facilitate interactions between spatially separated organisms. Plants produce a wide variety of VOCs that mediate multiple interactions with their environment, ranging from the attraction of pollinators and seed dispersers (Dudareva et al., 2004; Knudsen et al., 2006) to plant defense and plant-plant communication (Paré & Tumlinson, 1999; Mumm & Dicke, 2010). Although VOCs produced by microorganisms have received attention only in the past decade, these compounds have been long described in literature. Zoller and Clark (1921) reported for the first time the production of VOCs by bacteria of the dysentery group. Five years later, Russian researchers reported that the ‘soil air’ should be recognized as an organic constituent, equally important as the soil aqueous and solid phases (Curl & Truelove, 1986). Several studies from the late 1960s and early 1970s described the presence of ‘volatile inhibitors’ in soil. For example, microbial volatile organic and inorganic compounds were reported as major factors in soil fungistasis, the widespread soil characteristic that prevents viable fungal spores from germinating (Dobbs & Hinson, 1953). Fungistastic effects of the soil were relieved by partial sterilization and addition of antibiotics (Epstein & Lockwood, 1984), indicating that these VOC-mediated effects were of microbial origin. Hora and Baker (1972) demonstrated the production of a ‘volatile inhibitor’ of fungal spore germination in sterilized soils inoculated with soil actinomycetes and individual isolates of Trichoderma. Since then, several soil VOCs have been shown to reduce or inhibit spore germination and hyphal growth of fungi (Chuankun et al., 2004; van Agtmaal et al., 2015) and to influence plant growth and development (Vespermann et al., 2007; Bailly & Weisskopf, 2012). Diversity and biosynthesis of microbial volatiles Currently, more than 1000 bacterial and fungal VOCs have been described in literature (Effmert et al., 2012). Microbial VOCs typically include alkenes, alcohols, ketones, terpenes, benzenoids, pyrazines, acids, esters, and aldehydes (Piechulla & Degenhardt, 2014). Many of these compounds are produced by different soil and plant-associated bacteria and fungi (Fig. 1). Some of the microbial VOCs are common to several phylogenetic groups, while others seem to be unique for some species (Larsen & Frisvad, 1995; Schnürer et al., 1999; Muller et al., 2013). One of the most well-known microbial VOCs is geosmin, produced by most Streptomyces species, cyanobacteria and some fungi. Geosmin is a member of the terpene class of compounds and is responsible for the characteristic musty or earthy smell 10 | General introduction and thesis outline of moist soils (Gerber, 1968; Jiang et al., 2007). Although this compound has been identified already in 1891 and isolated in 1965, its ecological roles remain unknown to date (Berthelot & Andre, 1891; Gerber, 1968; Jiang et al., 2007). Microbial VOCs are produced via both primary and secondary metabolism (Korpi et al., 2009). The biosynthetic pathways involved in VOC production by microorganisms are carbon metabolism, fatty acid degradation, fermentation, amino acid catabolism, terpenoid biosynthesis, and sulfur metabolism (Peñuelas et al., 2014). Microbial production of aliphatic hydrocarbons is typically derived from fatty acids (Schulz & Dickschat, 2007). Decarboxylation of intermediates results in alkanes, alkenes or methyl ketones, whereas the reduction of the carboxyl group leads to the generation of aldehydes and alkanols (Peñuelas et al., 2014). Eight-carbon VOCs, such as 1-octen-3-ol and 3-octanone, are products of the oxidation and cleavage of the fatty acid linoleic acid, and classified as oxylipins (Combet et al., 2006). Acetoin (3-hydroxy-2-butanone) and its oxidized form 2,3- butanedione are derived from pyruvate fermentation under anaerobic conditions (Ryu et al., 2003; Audrain et al., 2015). Short-chain-branched alcohols, such as 3-methyl-1-butanol and 2-methyl-1- butanol, are produced by enzymatic conversion of branched chain amino acids via the Ehrlich pathway (Marilley & Casey, 2004). Aromatic hydrocarbons, such as 2-phenylethanol, are generated in bacteria and fungi via the shikimic acid pathway, with L-phenylalanine as a precursor (Hazelwood et al., 2008; Kim et al., 2014). The bacterial production of indole, another aromatic hydrocarbon, is regulated by several environmental factors such as the availability of extracellular tryptophan, cell population density, catabolite repression, temperature and pH (Lee & Lee, 2010). The indole biosynthetic pathway is well characterized in Escherichia coli, where tryptophanase encoded by tnaA converts tryptophan into indole, pyruvate and ammonia (Newton & Snell, 1965; Pittard, 1996). Aliphatic amino acids, such as glutamate, aspartate, alanine, valine, leucine, isoleucine and methionine, serve as precursors for bacterial VOCs. Decarboxylation of these amino acids followed by deamination results in their respective 2-keto acids. After decarboxylation and in the presence of 2-keto acid decarboxylase, they are then transformed into alcohols and/or into ethyl or methyl esters (Roze et al., 2010). Terpenes are the largest class of natural VOCs with over 50.000 known members (Conolly & Hill, 1991). They can mediate numerous antagonistic and beneficial interactions among (micro)organisms (Gershenzon & Dudareva, 2007; Dickschat et al., 2014). Fungi and bacteria produce a variety of terpenoids which are transformed and rearranged to a multitude of compounds (Kramer & Abraham, 2011; Cane & Ikeda, 2012; Song et al., 2015). Terpene synthases are the primary enzymes responsible for catalyzing the formation of CHAPTER ONE | 11 hemiterpenes (C5), monoterpenes (C10), sesquiterpenes (C15) or diterpenes (C20) from the substrates dimethylallyl diphosphate (DMAPP), geranyl diphosphate (GPP) farnesyl diphosphate (FPP) and geranylgeranly diphosphate (GGPP), respectively (Tholl, 2006; Dickschat et al., 2014). Several terpene cyclases and synthases have been identified by mining of bacterial genomes, including those involved in the biosynthesis of 2- methylisoborneol (2-MIB) and 2-methylenebornane (Komatsu et al., 2008; Chou et al., 2010; Moody et al., 2012; Yamada et al., 2015). Sulfur-containing VOCs range from relatively small compounds such as dimethyl sulfide, dimethyl disulphide and dimethyl trisulphide to more complex VOCs, such as 2- methyl-4,5-dihydrothiophene (Splivallo et al., 2011; Effmert et al., 2012). Two main biosynthetic pathways have been described for the production of sulfur-containing VOCs. The first pathway involves a one-step conversion of L-methionine to metanethiol by methionine lyases. The second one is initiated by L-methionine transamination to 4- methylthio- 2-oxobutyric acid, which is then converted to 3-(methylthio)propanal via decarboxylation or reduced to 4-methylthio-2-hydroxybutyric acid, with the ultimate formation of metanethiol (Bustos et al., 2011; Splivallo et al., 2011). Dimethyl sulfide is formed by the cleavage of dimethylsulfoniopropionate,
Recommended publications
  • Clemson University Tigerprints All Dissertations Dissertations 5-2014 Evaluation and Development of Nisin-Containing Packaging for Ready-To-Eat Meats, Utilizing Methods
    Clemson University TigerPrints All Dissertations Dissertations 5-2014 Evaluation and Development of Nisin-Containing Packaging for Ready-to-Eat Meats, Utilizing Methods Feasible for Future Commercialization Angela Morgan Clemson University Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Recommended Citation Morgan, Angela, "Evaluation and Development of Nisin-Containing Packaging for Ready-to-Eat Meats, Utilizing Methods Feasible for Future Commercialization" (2014). All Dissertations. 1769. https://tigerprints.clemson.edu/all_dissertations/1769 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. EVALUATION AND DEVELOPMENT OF NISIN-CONTAINING PACKAGING FOR READY-TO-EAT MEATS, UTILIZING METHODS FEASIBLE FOR FUTURE COMMERCIALIZATION ___________________________________________________________ A Dissertation Presented to the Graduate School of Clemson University ___________________________________________________________ In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Food Technology ___________________________________________________________ by Angela Morgan May 2014 ___________________________________________________________ Accepted by: Kay Cooksey, Ph.D., Committee Chair Terri Bruce, Ph.D. Duncan Darby, Ph.D. Aaron Brody, Ph.D. ABSTRACT Antimicrobial food packaging
    [Show full text]
  • Plant-To-Plant Communication Triggered by Systemin Primes Anti
    www.nature.com/scientificreports OPEN Plant-to-plant communication triggered by systemin primes anti- herbivore resistance in tomato Received: 10 February 2017 Mariangela Coppola1, Pasquale Cascone2, Valentina Madonna1, Ilaria Di Lelio1, Francesco Accepted: 27 October 2017 Esposito1, Concetta Avitabile3, Alessandra Romanelli 4, Emilio Guerrieri 2, Alessia Vitiello1, Published: xx xx xxxx Francesco Pennacchio1, Rosa Rao1 & Giandomenico Corrado1 Plants actively respond to herbivory by inducing various defense mechanisms in both damaged (locally) and non-damaged tissues (systemically). In addition, it is currently widely accepted that plant- to-plant communication allows specifc neighbors to be warned of likely incoming stress (defense priming). Systemin is a plant peptide hormone promoting the systemic response to herbivory in tomato. This 18-aa peptide is also able to induce the release of bioactive Volatile Organic Compounds, thus also promoting the interaction between the tomato and the third trophic level (e.g. predators and parasitoids of insect pests). In this work, using a combination of gene expression (RNA-Seq and qRT-PCR), behavioral and chemical approaches, we demonstrate that systemin triggers metabolic changes of the plant that are capable of inducing a primed state in neighboring unchallenged plants. At the molecular level, the primed state is mainly associated with an elevated transcription of pattern -recognition receptors, signaling enzymes and transcription factors. Compared to naïve plants, systemin-primed plants were signifcantly more resistant to herbivorous pests, more attractive to parasitoids and showed an increased response to wounding. Small peptides are nowadays considered fundamental signaling molecules in many plant processes and this work extends the range of downstream efects of this class of molecules to intraspecifc plant-to-plant communication.
    [Show full text]
  • Volatile Hydrocarbons from Endophytic Fungi and Their Efficacy in Fuel Production and Disease Control B
    Naik Egyptian Journal of Biological Pest Control (2018) 28:69 Egyptian Journal of https://doi.org/10.1186/s41938-018-0072-x Biological Pest Control REVIEW ARTICLE Open Access Volatile hydrocarbons from endophytic fungi and their efficacy in fuel production and disease control B. Shankar Naik Abstract Endophytic fungi are the microorganisms which asymptomatically colonize internal tissues of plant roots and shoots. Endophytes produce a broad spectrum of odorous compounds with different physicochemical and biological properties that make them useful in both industry and agriculture. Many endophytic fungi are known to produce a wide spectrum of volatile organic compounds with high densities, which include terpenes, flavonoids, alkaloids, quinines, cyclohexanes, and hydrocarbons. Many of these compounds showed anti-microbial, anti-oxidant, anti-neoplastic, anti-leishmanial and anti-proliferative activities, cytotoxicity, and fuel production. In this review, the role of volatile compounds produced by fungal endophytes in fuel production and their potential application in biological control is discussed. Keywords: Endophytic fungi, Biocontrol, Biofuel, Mycodiesel, Volatile organic compounds Background activities, and cytotoxicity (Firakova et al. 2007;Korpiet Endophytic fungi are the microorganisms, which asymp- al. 2009; Kharwar et al. 2011; Zhao et al. 2016 and Wu et tomatically colonize the internal tissues of plant roots and al. 2016). shoots (Bacon and White 2000). Endophytes provide Volatile organic compounds (VOCs) are a large group beneficial effects on host plants in deterring pathogens, of carbon-based chemicals with low molecular weights herbivores, increased tolerance to stress drought, low soil and high vapor pressure produced by living organisms as fertility, and enhancement of plant biomass (Redman et al.
    [Show full text]
  • Chapter 2 Molecular Plant Volatile Communication
    CHAPTER 2 MOLECULAR PLANT VOLATILE COMMUNICATION Jarmo K. Holopainen* and James D. Blande Department of Environmental Science, Kuopio, Campus, University of Eastern Finland, Kuopio, Finland *Corresponding Author: Jarmo K. Holopainen—Email: [email protected] Abstract: Plants produce a wide array of volatile organic compounds (VOCs) which have multiple functions as internal plant hormones (e.g., ethylene, methyl jasmonate and methyl salicylate), in communication with conspecific and heterospecific plants and in communication with organisms of second (herbivores and pollinators) and third (enemies of herbivores) trophic levels. Species specific VOCs normally repel polyphagous herbivores and those specialised on other plant species, but may attract specialist herbivores and their natural enemies, which use VOCs as host location cues. Attraction of predators and parasitoids by VOCs is considered an evolved indirect defence, whereby plants are able to indirectly reduce biotic stress caused by damaging herbivores. In this chapter we review these interactions where VOCs are known to play a crucial role. We then discuss the importance of volatile communication in self and nonself detection. VOCs are suggested to appear in soil ecosystems where distinction of own roots from neighbours roots is essential to optimise root growth, but limited evidence of above‑ground plant self‑recognition is available. INTRODUCTION Plants are literally rooted to the ground and therefore unable to change location. Consequently, they are easy targets to organisms that wish to feed on them. Plants have evolved a vast array of defensive features that effectively reduce the number of their enemies.1 However, defences are rarely flawless, meaning that plants cannot Not for Distribution ©2012 Copyright Landes Bioscience and Springer.
    [Show full text]
  • The Biosemiotics of Plant Communication
    The Biosemiotics of Plant Communication Günther Witzany Telos — Philosophische Praxis, Austria Abstract: This contribution demonstrates that the development and growth of plants depends on the success of complex communication processes. These communication processes are primarily sign-mediated interactions and are not simply an mechanical exchange of ‘information’, as that term has come to be understood (or misunderstood) in science. Rather, such interactions as I will be describing here involve the active coordination and organisation of a great variety of different behavioural patterns — all of which must be mediated by signs. Thus proposed, a biosemiotics of plant communication investigates com- munication processes both within and among the cells, tissues, and organs of plants as sign-mediated interactions which follow (1) combinatorial (syntactic), (2) context-sensitive (pragmatic) and (3) content-specific (semantic) levels of rules. As will be seen in the cases under investigation, the context of interactions in which a plant organism is interwoven determines the content arrangement of its response behaviour. And as exemplified by the multiply semiotic roles played by the plant hormone auxin that I will discuss below, this means that a molecule type of identical chemical structure may function in the instantiation of different meanings (semantics) that are determined by the different contexts (pragmatics) in which this sign is used. 1. Introduction iosemiotics investigates the use of signs within and between organ- isms. Such signs may be signals or symbols, and many of them are Bchemical molecules. In the highly developed eukaryotic kingdoms, the behavioural patterns of organisms may also serve as signs, as for example, the dances of bees.
    [Show full text]
  • Effects of Plant-Plant Airborne Interactions on Performance of Neighboring Plants Using Wild Types and Genetically Modified Lines of Arabidopsis Thaliana
    EFFECTS OF PLANT-PLANT AIRBORNE INTERACTIONS ON PERFORMANCE OF NEIGHBORING PLANTS USING WILD TYPES AND GENETICALLY MODIFIED LINES OF ARABIDOPSIS THALIANA Claire Thelen A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2020 Committee: Maria Gabriela Bidart, Advisor Heidi Appel Vipa Phuntumart ii ABSTRACT M. Gabriela Bidart, Advisor Understanding plant-plant communication further elucidates how plants interact with their environment, and how this communication can be manipulated for agricultural and ecological purposes. Part of understanding plant-plant communication is discovering the mechanisms behind plant-plant recognition, and whether plants can distinguish between genetically like and unlike neighbors. It has been previously shown that plants can “communicate” with neighboring plants through airborne volatile organic compounds (VOCs), which can act as signals related to different environmental stressors. This study focused on the interaction among different genotypes of the annual plant Arabidopsis thaliana. Specifically, a growth chamber experiment was performed to compare how different genotypes of neighboring plants impacted a focal plant’s fitness-related phenotypes and developmental stages. The focal plant genotype was wild type Col-0, and the neighboring genotypes included the wild type Landsberg (Ler-0), and the genetically modified (GM) genotypes: Etr1-1 and Jar1-1. These GM lines have a single point-mutation that impacts their ability to produce a particular VOC. This allows for the evaluation of a particular role that a VOC may have on plant-plant airborne communication. Plants were grown in separate pots to eliminate potential belowground interactions through the roots, and distantly positioned to avoid aboveground physical contact between plants.
    [Show full text]
  • Paenibacillaceae Cover
    The Family Paenibacillaceae Strain Catalog and Reference • BGSC • Daniel R. Zeigler, Director The Family Paenibacillaceae Bacillus Genetic Stock Center Catalog of Strains Part 5 Daniel R. Zeigler, Ph.D. BGSC Director © 2013 Daniel R. Zeigler Bacillus Genetic Stock Center 484 West Twelfth Avenue Biological Sciences 556 Columbus OH 43210 USA www.bgsc.org The Bacillus Genetic Stock Center is supported in part by a grant from the National Sciences Foundation, Award Number: DBI-1349029 The author disclaims any conflict of interest. Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or by the Ohio State University. Cover: Paenibacillus dendritiformus colony pattern formation. Color added for effect. Image courtesy of Eshel Ben Jacob. TABLE OF CONTENTS Table of Contents .......................................................................................................................................................... 1 Welcome to the Bacillus Genetic Stock Center ............................................................................................................. 2 What is the Bacillus Genetic Stock Center? ............................................................................................................... 2 What kinds of cultures are available from the BGSC? ............................................................................................... 2 What you can do to help the BGSC ...........................................................................................................................
    [Show full text]
  • Actinobacteria and Myxobacteria Isolated from Freshwater Snails and Other Uncommon Iranian Habitats, Their Taxonomy and Secondary Metabolism
    Actinobacteria and Myxobacteria isolated from freshwater snails and other uncommon Iranian habitats, their taxonomy and secondary metabolism Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades einer Doktorin der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Nasim Safaei aus Teheran / Iran 1. Referent: Professor Dr. Michael Steinert 2. Referent: Privatdozent Dr. Joachim M. Wink eingereicht am: 24.02.2021 mündliche Prüfung (Disputation) am: 20.04.2021 Druckjahr 2021 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Safaei, N. Mast, Y. Steinert, M. Huber, K. Bunk, B. Wink, J. (2020). Angucycline-like aromatic polyketide from a novel Streptomyces species reveals freshwater snail Physa acuta as underexplored reservoir for antibiotic-producing actinomycetes. J Antibiotics. DOI: 10.3390/ antibiotics10010022 Safaei, N. Nouioui, I. Mast, Y. Zaburannyi, N. Rohde, M. Schumann, P. Müller, R. Wink.J (2021) Kibdelosporangium persicum sp. nov., a new member of the Actinomycetes from a hot desert in Iran. Int J Syst Evol Microbiol (IJSEM). DOI: 10.1099/ijsem.0.004625 Tagungsbeiträge Actinobacteria and myxobacteria isolated from freshwater snails (Talk in 11th Annual Retreat, HZI, 2020) Posterbeiträge Myxobacteria and Actinomycetes isolated from freshwater snails and
    [Show full text]
  • The Rising of “Modern Actinobacteria” Era Jodi Woan-Fei Law1, Vengadesh Letchumanan1, Loh Teng-Hern Tan1, Hooi-Leng Ser1, Bey-Hing Goh2, Learn-Han Lee1*
    Review Article Progress in Microbes and Molecular Biology The Rising of “Modern Actinobacteria” Era Jodi Woan-Fei Law1, Vengadesh Letchumanan1, Loh Teng-Hern Tan1, Hooi-Leng Ser1, Bey-Hing Goh2, Learn-Han Lee1* 1Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia. 2Biofunctional Molecule Exploratory Research Group (BMEX), School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia. Abstract: The term “Modern Actinobacteria” (MOD-ACTINO) was coined by a Malaysian Scientist Dr. Lee Learn-Han, who has great expertise and experience in the field of actinobacteria research. MOD-ACTINO is defined as a group of actinobacteria capable of producing compounds that can be explored for modern applications such as development of new drugs and cosmeceutics. MOD-ACTINO members consist of already identified or novel actinobacteria isolated from special environments: mangrove, desert, lake, hot spring, cave, mountain, Arctic and Antarctic regions. These actinobac- teria are valuable sources for various industries which can contribute directly/indirectly towards the improvement in many aspects of our lives. Keywords: modern; bioactive; actinobacteria; *Correspondence: Learn-Han Lee, Novel Bacteria and environment; bioprospecting Drug Discovery Research Group (NBDD), Microbiome and Biore-source Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash Uni- Received: 16th February 2020 versity Malaysia, 47500 Bandar Sunway, Selangor Darul Accepted: 23rd March 2020 Ehsan, Malaysia. lee. [email protected] Published Online: 29th March 2020 Citation: Law JW-F, Letchumanan V, Tan LT-H et al.
    [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]
  • Comparative Fecal Metagenomics Unveils Unique Functional Capacity
    Lamendella et al. BMC Microbiology 2011, 11:103 http://www.biomedcentral.com/1471-2180/11/103 RESEARCHARTICLE Open Access Comparative fecal metagenomics unveils unique functional capacity of the swine gut Regina Lamendella1,4, Jorge W Santo Domingo2*, Shreya Ghosh1, John Martinson3 and Daniel B Oerther1,5 Abstract Background: Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health as well as to food and water safety due to the presence of human pathogens in pig feces. Nonetheless, limited information on the functional diversity of the swine gut microbiome is available. Results: Analysis of 637, 722 pyrosequencing reads (130 megabases) generated from Yorkshire pig fecal DNA extracts was performed to help better understand the microbial diversity and largely unknown functional capacity of the swine gut microbiome. Swine fecal metagenomic sequences were annotated using both MG-RAST and JGI IMG/M-ER pipelines. Taxonomic analysis of metagenomic reads indicated that swine fecal microbiomes were dominated by Firmicutes and Bacteroidetes phyla. At a finer phylogenetic resolution, Prevotella spp. dominated the swine fecal metagenome, while some genes associated with Treponema and Anareovibrio species were found to be exclusively within the pig fecal metagenomic sequences analyzed. Functional analysis revealed that carbohydrate metabolism was the most abundant SEED subsystem, representing 13% of the swine metagenome. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Virulence factors associated with antibiotic resistance genes with highest sequence homology to genes in Bacteroidetes, Clostridia, and Methanosarcina were numerous within the gene families unique to the swine fecal metagenomes.
    [Show full text]
  • Influence of Temperature, Inoculation Interval, and Dosage on Biofumigation with Muscodor Albus to Control Postharvest Gray Mold on Grapes
    Influence of Temperature, Inoculation Interval, and Dosage on Biofumigation with Muscodor albus to Control Postharvest Gray Mold on Grapes F. Mlikota Gabler, Institute for Adriatic Crops, Put Duilova 11, 21000 Split, Croatia; R. Fassel, PACE International, LLC, Visalia, CA 93291; J. Mercier, AgraQuest Inc., Davis, CA 95616; and J. L. Smilanick, United States Depart- ment of Agriculture–Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648 trol gray mold are needed that are safe, ABSTRACT effective, and economical (1,15,16,21,23). Mlikota Gabler, F., Fassel, R., Mercier, J., and Smilanick, J. L. 2006. Influence of temperature, Alternatives to sulfur dioxide for control of inoculation interval, and dosage on biofumigation with Muscodor albus to control postharvest postharvest gray mold include near-harvest gray mold on grapes. Plant Dis. 90:1019-1025. ethanol or biological control agent applica- tions (11,15) and postharvest immersion of Control of postharvest gray mold, caused by Botrytis cinerea, on Thompson Seedless grape by grapes in bicarbonates, chlorine, ethanol, biofumigation with a rye grain formulation of Muscodor albus, a fungus that produces volatiles or heated water (14,16,21,23). However, lethal to many microorganisms, was evaluated. The influences of temperature, biofumigant dos- methods requiring additional postharvest age, and interval between inoculation and treatment on disease incidence and severity on de- tached single berries were assessed. When biofumigation began within 24 h after inoculation, processing and handling increase costs and higher M. albus dosages (≥50 g of the M. albus grain formulation per kilogram of grapes at 20ºC could alter the appearance of the berries or or 100 g/kg at 5ºC) stopped infections and control persisted after M.
    [Show full text]