Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era
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Agricultural Bioterrorism
From the pages of Recent titles Agricultural Bioterrorism: A Federal Strategy to Meet the Threat Agricultural in the McNair MCNAIR PAPER 65 Bioterrorism: Paper series: A Federal Strategy to Meet the Threat 64 The United States ignores the The Strategic Implications of a Nuclear-Armed Iran Agricultural potential for agricultural bioter- Kori N. Schake and rorism at its peril. The relative Judith S. Yaphe Bioterrorism: ease of a catastrophic bio- weapons attack against the 63 A Federal Strategy American food and agriculture All Possible Wars? infrastructure, and the devastat- Toward a Consensus View of the Future Security to Meet the Threat ing economic and social conse- Environment, 2001–2025 quences of such an act, demand Sam J. Tangredi that the Nation pursue an aggres- sive, focused, coordinated, and 62 stand-alone national strategy to The Revenge of the Melians: Asymmetric combat agricultural bioterrorism. Threats and the Next QDR The strategy should build on Kenneth F. McKenzie, Jr. counterterrorism initiatives already underway; leverage exist- 61 ing Federal, state, and local pro- Illuminating HENRY S. PARKER grams and capabilities; and Tomorrow’s War Martin C. Libicki involve key customers, stake- PARKER holders, and partners. The U.S. 60 Department of Agriculture The Revolution in should lead the development of Military Affairs: this strategy. Allied Perspectives Robbin F. Laird and Holger H. Mey Institute for National Strategic Studies National Defense University About the Author NATIONAL DEFENSE UNIVERSITY President: Vice Admiral Paul G. Gaffney II, USN Henry S. Parker is National Program Leader for Aquaculture at the Vice President: Ambassador Robin Lynn Raphel Agricultural Research Service in the U.S. -
The Study on the Cultivable Microbiome of the Aquatic Fern Azolla Filiculoides L
applied sciences Article The Study on the Cultivable Microbiome of the Aquatic Fern Azolla Filiculoides L. as New Source of Beneficial Microorganisms Artur Banach 1,* , Agnieszka Ku´zniar 1, Radosław Mencfel 2 and Agnieszka Woli ´nska 1 1 Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, 20-708 Lublin, Poland; [email protected] (A.K.); [email protected] (A.W.) 2 Department of Animal Physiology and Toxicology, The John Paul II Catholic University of Lublin, 20-708 Lublin, Poland; [email protected] * Correspondence: [email protected]; Tel.: +48-81-454-5442 Received: 6 May 2019; Accepted: 24 May 2019; Published: 26 May 2019 Abstract: The aim of the study was to determine the still not completely described microbiome associated with the aquatic fern Azolla filiculoides. During the experiment, 58 microbial isolates (43 epiphytes and 15 endophytes) with different morphologies were obtained. We successfully identified 85% of microorganisms and assigned them to 9 bacterial genera: Achromobacter, Bacillus, Microbacterium, Delftia, Agrobacterium, and Alcaligenes (epiphytes) as well as Bacillus, Staphylococcus, Micrococcus, and Acinetobacter (endophytes). We also studied an A. filiculoides cyanobiont originally classified as Anabaena azollae; however, the analysis of its morphological traits suggests that this should be renamed as Trichormus azollae. Finally, the potential of the representatives of the identified microbial genera to synthesize plant growth-promoting substances such as indole-3-acetic acid (IAA), cellulase and protease enzymes, siderophores and phosphorus (P) and their potential of utilization thereof were checked. Delftia sp. AzoEpi7 was the only one from all the identified genera exhibiting the ability to synthesize all the studied growth promoters; thus, it was recommended as the most beneficial bacteria in the studied microbiome. -
Optimize the Plant Microbiota to Increase Plant Growth and Health
July 2019 POSITION PAPER Optimize the plant microbiota to increase plant growth and health Barret M. (INRA, IRHS), Dufour P. (RAGT), Durand-Tardif M. (GIS BV), Mariadassou M. (INRA, MaIAGE), Mougel C. (INRA, IGEPP), Perez P. (Limagrain), Roumagnac P. (Cirad, BGPI), Sanguin H. (Cirad, BGPI), Steinberg C. (INRA, Agroécologie), Szambien M. (GIS BV) The “Groupement d’Intérêt Scientifique Biotechnologies Vertes” (GIS BV) organized on November 13th, 2018 in Paris, a scientific workshop on “Metagenomics for agro-ecosystems management and plant breeding”. Thirty-four scientists, including eight from the private sector attended the workshop. General discussion was organized around the presentations related to plant, seeds and soil microbiota, and data treatment to reconstruct interaction networks. This article gathers the current French research strengths, relative to the international context and highlights the research priorities between the public and the private sectors, using plant genetics and plant-microbiota interactions for the benefit of future agricultures. plant productivity. Hence, over recent years a Socio-economic context, scientific number of research groups explored the impact of challenges and opportunities environmental factors and host genetic variation on the composition and dynamics of plant microbiota [12–19]. Overall, these studies Plants live in association with a wide diverse and acknowledged an important influence of the complex assembly of viruses and microorganisms environment on plant microbiota composition and including -
Recent Developments in the Study of Plant Microbiomes
microorganisms Review Recent Developments in the Study of Plant Microbiomes Bernard R. Glick 1 and Elisa Gamalero 2,* 1 Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; [email protected] 2 Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel, 11, 15121 Alessandria, Italy * Correspondence: [email protected] Abstract: To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia with the collective being responsible for the positive effects on plant growth. Different plants attract different cross-sections of the bacteria and fungi in the soil, initially based on the composition of the unique root exudates from each plant. Thus, plants mostly attract those microorganisms that are beneficial to plants and exclude those that are potentially pathogenic. Beneficial bacterial consortia not only help to promote plant growth, these consortia also protect plants from a wide range of direct and indirect environmental stresses. Moreover, it is currently possible to engineer plant seeds to contain desired bacterial strains and thereby benefit the next generation of plants. In this way, it may no longer be necessary to deliver beneficial microbiota to each individual growing plant. As we develop a better understanding of beneficial bacterial microbiomes, it may become possible to develop synthetic microbiomes where compatible bacteria work together to facilitate plant growth under a wide range of natural conditions. Keywords: soil bacteria; plant growth-promoting bacteria; PGPB; seed microbiomes; root micro- Citation: Glick, B.R.; Gamalero, E. -
"Plant Microbiome Identification and Characterization". In: Current
Plant Microbiome Identification and Characterization Sarah L. Lebeis1 1Department of Microbiology, University of Tennessee, Knoxville, Tennessee To fully exploit the potential of plant microbiome alterations to improve plant health, reliable methods must be used to prepare and characterize microbiome samples. The power of culture-independent studies is that they allow the charac- terization of novel microbial community members, but only microbial members consistently represented between different research groups are likely to become broadly applicable treatments. The identification of plant microbiome mem- bers can be affected by several experimental stages, including design, sample preparation, nucleic acid extraction, sequencing, and analysis. The protocols described here therefore aim to highlight crucial steps that experimenters should consider before beginning a plant microbiome study. C 2017 by John Wiley & Sons, Inc. Keywords: epiphyte r endophyte r plant microbiomes r phyllosphere r rhizosphere How to cite this article: Lebeis, S. L. (2017). Plant microbiome identification and characterization. Current Protocols in Plant Biology, 2, 135–146. doi: 10.1002/cppb.20048 INTRODUCTION As with any type of scientific research, it is imperative to develop clearly defined hy- potheses and experimental procedures to yield supporting or refuting data. The most common first set of studies to characterize a plant microbiome is amplicon sequencing of phylogenetically informative marker genes, such as bacterial and archaeal 16S ribosomal RNA (Caporaso et al., 2012), eukaryotic 18S rRNA (Stoeck et al., 2010), and the fungal intergenic transcribed spacer (ITS; Menkis et al., 2012). Without clear predictions, results are merely descriptive, which is especially dangerous when the phenotypes are inherently complex, such as clusters of sequences into Operational Taxonomic Units (OTUs) and their relative abundances. -
Investigating the Biology of Plant Infection by Magnaporthe Oryza
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Fungal Molecular Plant-Microbe Interactions Plant Pathology Department 2009 Under Pressure: Investigating the Biology of Plant Infection by Magnaporthe oryza Nicholas J. Talbot University of Exeter, [email protected] Richard A. Wilson University of Nebraska - Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/plantpathfungal Part of the Plant Pathology Commons Talbot, Nicholas J. and Wilson, Richard A., "Under Pressure: Investigating the Biology of Plant Infection by Magnaporthe oryza" (2009). Fungal Molecular Plant-Microbe Interactions. 7. https://digitalcommons.unl.edu/plantpathfungal/7 This Article is brought to you for free and open access by the Plant Pathology Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Fungal Molecular Plant- Microbe Interactions by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Nature Reviews: Microbiology (March 2009) 7: 185-195. Copyright 2009, Macmillan. DOI: 10.1038/nrmicro2032. Used by permission. Reviews Under Pressure: Investigating the Biology of Plant Infection by Magnaporthe oryza Richard A. Wilson and Nicholas J. Talbot School of Biosciences, University of Exeter, Exeter, United Kingdom; correspondence to [email protected] Wilson, affiliation 2012: University of Nebraska-Lincoln, Lincoln, Nebraska, U.S.A.; [email protected] Abstract The filamentous fungus Magnaporthe oryzae causes rice blast, the most serious disease of cultivated rice. Cellular differentia- tion of M. oryzae forms an infection structure called the appressorium, which generates enormous cellular turgor that is suffi- cient to rupture the plant cuticle. Here, we show how functional genomics approaches are providing new insight into the ge- netic control of plant infection by M. -
Host-Microbiota Interactions: from Holobiont Theory to Analysis Jean-Christophe Simon1* , Julian R
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Online Research @ Cardiff Simon et al. Microbiome (2019) 7:5 https://doi.org/10.1186/s40168-019-0619-4 COMMENTARY Open Access Host-microbiota interactions: from holobiont theory to analysis Jean-Christophe Simon1* , Julian R. Marchesi2,3, Christophe Mougel1 and Marc-André Selosse4,5 Abstract In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host- associated microbes and their central role in host biology, ecology, and evolution. Through this special series “Host-microbiota interactions: from holobiont theory to analysis,” we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts. Keywords: Host-microbiota interactions, Holobiont, Hologenome, Metagenomics, Symbiosis Background the National Center for Scientific Research (CNRS), the It is becoming increasingly clear that the development, National Institute for Agricultural Research (INRA), growth, and health (in one word, all functions) of and the National Museum of Natural History (MNHN). -
The Plant Microbiome Explored: Implications for Experimental Botany
Journal of Experimental Botany, Vol. 67, No. 4 pp. 995–1002, 2016 doi:10.1093/jxb/erv466 Advance Access publication 7 November 2015 REVIEW PAPER The plant microbiome explored: implications for experimental botany Gabriele Berg1,2, Daria Rybakova1, Martin Grube3 and Martina Köberl1,4 1 Graz University of Technology, Institute of Environmental Biotechnology, 8010 Graz, Austria 2 Austrian Centre of Industrial Biotechnology (ACIB GmbH), 8010 Graz, Austria 3 University of Graz, Institute of Plant Sciences, 8010 Graz, Austria 4 Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA 99352, USA Received 20 July 2015; Accepted 5 October 2015 Editor: Adam Price, University of Aberdeen Abstract The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habi- tats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorgan- isms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are co- evolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. -
Streptomyces with Antifungal Activity Against Rice Blast Causing Fungus, Magnaporthe Grisea
J. Microbiol. Biotechnol. (2002), 12(6), 1026–1028 Streptomyces with Antifungal Activity Against Rice Blast Causing Fungus, Magnaporthe grisea LEE, CHUL-HOON2, BUM-JOON KIM3, GYUNG JA CHOI4, KWANG YUN CHO4, HEEJUNG YANG1, 1 1 1 CHOONSHIK SHIN ,SHINYOUNG MIN , AND YOONGHO LIM 1Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Korea 2Department of Medical Genetics & Institute of Biomedical Science, College of Medicine, Hanyang University, Seoul 133-791, Korea 3Medical School, Cheju National University, Jeju 690-756, Korea 4Screening Division, Korea Research Institute of Chemical Technology, Daejon 305-600, Korea Received: November 5, 2002 Accepted: November 26, 2002 Abstract Screening tests against fungus causing rice blast, samples were collected during 2001 at several sites near Magnaporthe grisea, were performed in order to develop Hanla Mountain, on Jeju Island, Korea. Samples were used biopesticides. More than 400 actinomycetes collected at several as substrates for isolation of actinomycetes that exhibited sites near Hanla Mountain on Jeju Island, Korea were tested, antifungal activities. The isolation medium was starch- and strain BG2-53 showed potent antifungal activity. The casein agar. Autoclaved cyclohexamide was added to the in vivo screening was performed with fermentation broth, and isolation medium (50 µg/ml) for inhibition of fungal growth, the strain taxon was identified. and sterilized heat-labile nystatin (50 µg/ml) was also added. Key words: In vivo antifungal activities, Magnaporthe grisea, The final pH of the medium for isolation of actinomycetes rice blast, Streptomyces was adjusted to 7.0- 7.2. Approximately 1 g of soil was ground in a petri dish and heated at 60oC for 90 min in a drying oven. -
The Growing Threat of Biological Weapons
A reprint from American Scientist the magazine of Sigma Xi, The Scientific Research Society This reprint is provided for personal and noncommercial use. For any other use, please send a request to Permissions, American Scientist, P.O. Box 13975, Research Triangle Park, NC, 27709, U.S.A., or by electronic mail to [email protected]. ©Sigma Xi, The Scientific Research Society and other rightsholders The Growing Threat of Biological Weapons The terrorist threat is very real, and it’s about to get worse. Scientists should concern themselves before it’s too late Steven M. Block or half a century, America has par- cal development and use of biological um (Bacillus anthracis). Pasteur devel- F ticipated with the world’s nuclear weapons, as well as some recent trends oped the first animal vaccine against powers in an uneasy standoff of mutu- in their evolution and the prospects for anthrax, which, together with Lister’s ally assured destruction. Despite the containing their proliferation. ideas about antiseptic precautions, seemingly relentless proliferation of nu- helped turn the tide against outbreaks clear arms, there’s reason to hope that The Plague and Anthrax of the disease. some version of the current stalemate Biological warfare is not a new phe- Anthrax is only weakly communica- will continue to hold. Against this back- nomenon. The ancient Romans, and ble in humans and rarely causes dis- drop, terrorist factions and “nations of others before them, threw carrion into ease, unless the bacterium comes into concern” (the current government eu- wells to poison their adversaries’ contact with the bloodstream through a phemism for rogue states) have sought drinking water. -
Interagency Strategic Plan for Microbiome Research FY 2018-2022
Interagency Strategic Plan for Microbiome Research FY 2018-2022 April 2018 1 About this Document This plan was developed by the Microbiome Interagency Working Group (MIWG), an interagency working group under the Life Sciences Subcommittee (LSSC) of the National Science and Technology Council (NSTC) Committee on Science (CoS). The MIWG is a successor to the Fast Track Action Committee on Mapping the Microbiome (FTAC-MM). About the Fast Track Action Committee on Mapping the Microbiome The Fast Track Action Committee on Mapping the Microbiome (FTAC-MM) was established in February 2015 by action of the LSSC. The FTAC-MM released a report in November 2015 identifying areas of current Federal investment, research needs, and resource gaps for the development of an integrated Federal plan for microbiome research. The report identified priority areas for Federal agency coordination and cooperation on achieving a predictive understanding of microbiomes and their functions. About the Microbiome Interagency Working Group The Microbiome Interagency Working Group (MIWG) serves as part of the internal deliberative process of the NSTC and provides overall guidance and direction for microbiome research across the Federal government agencies. The MIWG was chartered in February 2016 to develop a Federal Strategic Plan for microbiome research. Using the FTAC-MM report as a foundation, the MIWG developed the Interagency Strategic Plan for Microbiome Research, taking into account how future Federal actions could benefit from an understanding of and engagement with current international activities. The Interagency Strategic Plan provides recommendations for improving coordination of microbiome research among Federal agencies and between agencies and non-Federal domestic and international microbiome research efforts. -
Enhanced Disease Resistance Conferred by Expression of An
Enhanced resistance to the rice blast fungus Magnaporthe grisea conferred by expression of a cecropin A gene in transgenic rice María Coca1, Gisela Peñas2, Jorge Gómez1, Sonia Campo1, Cristina Bortolotti1, Joaquima Messeguer2 and Blanca San Segundo1. Laboratorio de Genética Molecular Vegetal, Consorcio CSIC-IRTA; 1Departamento de Genética Molecular, Instituto de Biología Molecular de Barcelona, CSIC. Jordi Girona 18, 08034 Barcelona, Spain; 2Departamento de Genética Vegetal, IRTA Centro de Cabrils. Carretera de Cabrils s/n, Cabrils 08348, Barcelona, Spain Corresponding author: María Coca E-mail: [email protected] Tel: 34934006128 FAX: 34932045904 1 Abstract Cecropins are a family of antimicrobial peptides which constitute an important key component of the immune response in insects. Here, we demonstrate that transgenic rice (Oryza sativa L.) plants expressing the cecropin A gene from the giant silk moth Hyalophora cecropia show enhanced resistance to Magnaporthe grisea, the causal agent of the rice blast disease. Two plant codon-optimized synthetic cecropin A genes which were designed either to retain the cecropin A peptide in the endoplasmic reticulum, the ER-CecA gene, or to secrete cecropin A to the extracellular space, the Ap- CecA gene, were prepared. Both cecropin A genes were efficiently expressed in transgenic rice. The inhibitory activity of protein extracts prepared from leaves of cecropin A-expressing plants on the in vitro growth of M. grisea indicated that the cecropin A protein produced by the transgenic rice plants was biologically active. Whereas no effect on plant phenotype was observed in ER-CecA plants, most of the rice lines expressing the Ap-CecA gene were non fertile.