Characterization of Wheat Genotypes As Sources of Ice Nucleation Active
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The Microbiota Continuum Along the Female Reproductive Tract and Its Relation to Uterine-Related Diseases
ARTICLE DOI: 10.1038/s41467-017-00901-0 OPEN The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases Chen Chen1,2, Xiaolei Song1,3, Weixia Wei4,5, Huanzi Zhong 1,2,6, Juanjuan Dai4,5, Zhou Lan1, Fei Li1,2,3, Xinlei Yu1,2, Qiang Feng1,7, Zirong Wang1, Hailiang Xie1, Xiaomin Chen1, Chunwei Zeng1, Bo Wen1,2, Liping Zeng4,5, Hui Du4,5, Huiru Tang4,5, Changlu Xu1,8, Yan Xia1,3, Huihua Xia1,2,9, Huanming Yang1,10, Jian Wang1,10, Jun Wang1,11, Lise Madsen 1,6,12, Susanne Brix 13, Karsten Kristiansen1,6, Xun Xu1,2, Junhua Li 1,2,9,14, Ruifang Wu4,5 & Huijue Jia 1,2,9,11 Reports on bacteria detected in maternal fluids during pregnancy are typically associated with adverse consequences, and whether the female reproductive tract harbours distinct microbial communities beyond the vagina has been a matter of debate. Here we systematically sample the microbiota within the female reproductive tract in 110 women of reproductive age, and examine the nature of colonisation by 16S rRNA gene amplicon sequencing and cultivation. We find distinct microbial communities in cervical canal, uterus, fallopian tubes and perito- neal fluid, differing from that of the vagina. The results reflect a microbiota continuum along the female reproductive tract, indicative of a non-sterile environment. We also identify microbial taxa and potential functions that correlate with the menstrual cycle or are over- represented in subjects with adenomyosis or infertility due to endometriosis. The study provides insight into the nature of the vagino-uterine microbiome, and suggests that sur- veying the vaginal or cervical microbiota might be useful for detection of common diseases in the upper reproductive tract. -
Presence Absence Polymorphism for Alternative Pathogenicity Islands In
Presence͞absence polymorphism for alternative pathogenicity islands in Pseudomonas viridiflava, a pathogen of Arabidopsis Hitoshi Araki†‡, Dacheng Tian§, Erica M. Goss†, Katrin Jakob†, Solveig S. Halldorsdottir†, Martin Kreitman†, and Joy Bergelson†¶ †Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637; and §Department of Biology, Nanjing University, Nanjing 210093, Republic of China Communicated by Tomoko Ohta, National Institute of Genetics, Mishima, Japan, March 1, 2006 (received for review January 25, 2006) The contribution of arms race dynamics to plant–pathogen coevo- pathogens are defined and differentiated from close relatives by lution has been called into question by the presence of balanced horizontally acquired virulence factors (12). However, a survey polymorphisms in resistance genes of Arabidopsis thaliana, but of effectors in Pseudomonas syringae finds effectors that have less is known about the pathogen side of the interaction. Here we been acquired recently and others that have been transmitted investigate structural polymorphism in pathogenicity islands (PAIs) predominantly by descent, indicating that pathogenicity may in Pseudomonas viridiflava, a prevalent bacterial pathogen of A. evolve in both genomic contexts (13). thaliana. PAIs encode the type III secretion system along with its In this study, we investigated PAIs in P. viridiflava, which is a effectors and are essential for pathogen recognition in plants. P. prevalent bacterial pathogen of wild A. thaliana populations viridiflava harbors two structurally distinct and highly diverged PAI (14). P. viridiflava is in the P. syringae group (15). Although P. paralogs (T- and S-PAI) that are integrated in different chromo- syringae is intensively studied as a bacterial plant pathogen (13, some locations in the P. -
Bacteria Occurring in Onion (Allium Cepa L.) Foliage in Puerto Rico1-2 Juan Calle-Bellido3, Lydia I
Bacteria occurring in onion (Allium cepa L.) foliage in Puerto Rico1-2 Juan Calle-Bellido3, Lydia I. Rivera-Vargas4, Myrna Alameda4 and Irma Cabrera5 J. Agrie. Univ. P.R. 96(3-4):199-219 (2012) ABSTRACT Bacteria associated with foliar symptoms of onion (Allium cepa L.) were examined in the southern region of Puerto Rico from January through April 2004. Different symptoms were observed in onion foliage of cultivars 'Mercedes' and 'Excalibur' at Juana Díaz and Santa Isabel, Puerto Rico. Ellipsoidal sunken lesions with soft rot and disruption of tissue were the most common symptoms observed in onion foliage in field conditions. From a total of 39 bacterial strains isolated from diverse symptoms in onion foliage, 38% were isolated from soft rotting lesions. Ninety-two percent of the bacteria isolated from onion foliage was Gram negative. Pantoea spp. with 25%, was the most frequently isolated genus, followed by Pasteurella spp. and Serratia rubidae with 10% each. Fifty- six percent of the strains held plant pathogenic potential; these strains belong to the genera Acidovorax sp., Burkholderia sp., Clavibacter sp., Curtobacterium sp., Enterobacter sp., Pantoea spp., Pseudomonas spp., and Xanthomonas spp. Pathogenicity tests showed that seven out of eight tested bacterial strains evaluated under field conditions caused symptoms in onion foliage for both cultivars. Acidovorax avenae subsp. citrulli, Burkholderia glumae, Pantoea agglomerans, P. dispersa, Pseudomonas sp., Xanthomonas sp., and Xanthomonas-Wke sp. were pathogenic to leaf tissues. Clavibacter michiganensis was not pathogenic to leaf tissues. Other bacteria identified as associated with onion leaf tissue were Curtobacterium flaccumfaciens, Cytophaga sp., Enterobacter cloacae, Flavimonas oryzihabitans, Mannheimia haemolytica, Pantoea stewartii, Pasteurella anatis, P. -
Bacteria Associated with Vascular Wilt of Poplar
Bacteria associated with vascular wilt of poplar Hanna Kwasna ( [email protected] ) Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu https://orcid.org/0000-0001- 6135-4126 Wojciech Szewczyk Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Marlena Baranowska Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Jolanta Behnke-Borowczyk Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Research Article Keywords: Bacteria, Pathogens, Plantation, Poplar hybrids, Vascular wilt Posted Date: May 27th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-250846/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/30 Abstract In 2017, the 560-ha area of hybrid poplar plantation in northern Poland showed symptoms of tree decline. Leaves appeared smaller, turned yellow-brown, and were shed prematurely. Twigs and smaller branches died. Bark was sunken and discolored, often loosened and split. Trunks decayed from the base. Phloem and xylem showed brown necrosis. Ten per cent of trees died in 1–2 months. None of these symptoms was typical for known poplar diseases. Bacteria in soil and the necrotic base of poplar trunk were analysed with Illumina sequencing. Soil and wood were colonized by at least 615 and 249 taxa. The majority of bacteria were common to soil and wood. The most common taxa in soil were: Acidobacteria (14.757%), Actinobacteria (14.583%), Proteobacteria (36.872) with Betaproteobacteria (6.516%), Burkholderiales (6.102%), Comamonadaceae (2.786%), and Verrucomicrobia (5.307%).The most common taxa in wood were: Bacteroidetes (22.722%) including Chryseobacterium (5.074%), Flavobacteriales (10.873%), Sphingobacteriales (9.396%) with Pedobacter cryoconitis (7.306%), Proteobacteria (73.785%) with Enterobacteriales (33.247%) including Serratia (15.303%) and Sodalis (6.524%), Pseudomonadales (9.829%) including Pseudomonas (9.017%), Rhizobiales (6.826%), Sphingomonadales (5.646%), and Xanthomonadales (11.194%). -
Characterisation of Pseudomonas Spp. Isolated from Foods
07.QXD 9-03-2007 15:08 Pagina 39 Annals of Microbiology, 57 (1) 39-47 (2007) Characterisation of Pseudomonas spp. isolated from foods Laura FRANZETTI*, Mauro SCARPELLINI Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, sezione Microbiologia Agraria Alimentare Ecologica, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy Received 30 June 2006 / Accepted 27 December 2006 Abstract - Putative Pseudomonas spp. (102 isolates) from different foods were first characterised by API 20NE and then tested for some enzymatic activities (lipase and lecithinase production, starch hydrolysis and proteolytic activity). However subsequent molecular tests did not always confirm the results obtained, thus highlighting the limits of API 20NE. Instead RFLP ITS1 and the sequencing of 16S rRNA gene grouped the isolates into 6 clusters: Pseudomonas fluorescens (cluster I), Pseudomonas fragi (cluster II and V) Pseudomonas migulae (cluster III), Pseudomonas aeruginosa (cluster IV) and Pseudomonas chicorii (cluster VI). The pectinolytic activity was typical of species isolated from vegetable products, especially Pseudomonas fluorescens. Instead Pseudomonas fragi, predominantly isolated from meat was characterised by proteolytic and lipolytic activities. Key words: Pseudomonas fluorescens, enzymatic activity, ITS1. INTRODUCTION the most frequently found species, however the species dis- tribution within the food ecosystem remains relatively The genus Pseudomonas is the most heterogeneous and unknown (Arnaut-Rollier et al., 1999). The principal micro- ecologically significant group of known bacteria, and bial population of many vegetables in the field consists of includes Gram-negative motile aerobic rods that are wide- species of the genus Pseudomonas, especially the fluores- spread throughout nature and characterised by elevated cent forms. -
Microbial Genomic Sequencing Perspectives of the American Phytopathological Society (Revised 2008)
Microbial Genomic Sequencing Perspectives of the American Phytopathological Society (Revised 2008) The American Phytopathological Society 3340 Pilot Knob Road St. Paul, MN 55121-2097 Phone: +1.651.454.7250 Fax: +1.651.454.0766 Email: [email protected] APSnet: www.apsnet.org 1 Microbial Genomic Sequencing Perspectives of the American Phytopathological Society Background Microorganisms play a critical role in plant health. Depending on the organism, they can cause multiple diseases or prevent them. Yet, on a genomic level, we know little about them (The Microbe Project, 2001, National Science and Technology Council, Office of Science and Technology Policy, Washington, D.C., 29 pg.). Genomic analyses of plant associated microorganisms are as essential to understanding the development and suppression of plant diseases. Analyses of microbial genomes will complement those done on plant genomes (e.g. for Arabidopsis, rice, etc) by providing new insights into the nature of plant-microbe interactions. The APS has consulted its members and constituencies on priority setting of microorganisms that should be sequenced. A first list was compiled in 2000-2001which had significant impact in stimulating efforts leading to the sequencing of a number of microbial genomes, particularly bacterial and fungal. The list was revised in 2003. Researchers have been quite successful over the past two years in obtaining funding to sequence plant-associated microbes (see Existing sequencing projects with Plant-Associated Microbes), and therefore the list required a second revision in 2005 and a third in 2007. Nevertheless, there remains a critical need for greater information in microbial genomics. Thus it is with a sense of continued urgency that this 2008 revised list, created with extensive input from the membership of The American Phytopathological Society during 2007 is presented. -
Aquatic Microbial Ecology 80:15
The following supplement accompanies the article Isolates as models to study bacterial ecophysiology and biogeochemistry Åke Hagström*, Farooq Azam, Carlo Berg, Ulla Li Zweifel *Corresponding author: [email protected] Aquatic Microbial Ecology 80: 15–27 (2017) Supplementary Materials & Methods The bacteria characterized in this study were collected from sites at three different sea areas; the Northern Baltic Sea (63°30’N, 19°48’E), Northwest Mediterranean Sea (43°41'N, 7°19'E) and Southern California Bight (32°53'N, 117°15'W). Seawater was spread onto Zobell agar plates or marine agar plates (DIFCO) and incubated at in situ temperature. Colonies were picked and plate- purified before being frozen in liquid medium with 20% glycerol. The collection represents aerobic heterotrophic bacteria from pelagic waters. Bacteria were grown in media according to their physiological needs of salinity. Isolates from the Baltic Sea were grown on Zobell media (ZoBELL, 1941) (800 ml filtered seawater from the Baltic, 200 ml Milli-Q water, 5g Bacto-peptone, 1g Bacto-yeast extract). Isolates from the Mediterranean Sea and the Southern California Bight were grown on marine agar or marine broth (DIFCO laboratories). The optimal temperature for growth was determined by growing each isolate in 4ml of appropriate media at 5, 10, 15, 20, 25, 30, 35, 40, 45 and 50o C with gentle shaking. Growth was measured by an increase in absorbance at 550nm. Statistical analyses The influence of temperature, geographical origin and taxonomic affiliation on growth rates was assessed by a two-way analysis of variance (ANOVA) in R (http://www.r-project.org/) and the “car” package. -
A Pseudomonas Viridiflava-Related Bacterium Causes a Dark-Reddish
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Repositorio Institucional de la Universidad de Oviedo A Pseudomonas viridiflava-Related Bacterium Causes a Dark-Reddish Spot Disease in Glycine max Ana J. González,a Ana M. Fernández,a Mateo San José,b Germán González-Varela,a and M. Rosario Rodiciob Downloaded from Laboratorio de Fitopatología, Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Villaviciosa, Asturias, Spain,a and Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Asturias, Spainb A virulent Pseudomonas viridiflava-related bacterium has been identified as a new pathogen of soybean, one of the most impor- tant crops worldwide. The bacterium was recovered from forage soybean leaves with dark-reddish spots, and damage on petioles and pods was also observed. In contrast, common bean was not affected. http://aem.asm.org/ oybean (Glycine max [L.] Mer. In), a subtropical leguminous related (99% identity) to 16S rRNA gene sequences of P. viri- Splant native to southeastern Asia, is one of the most important diflava (accession no. AM909660), Pseudomonas corrugata crops for both human food and animal feed worldwide. Three (AF348508), and Pseudomonas tolaasii (AF348507). However, the bacterial species are recognized as soybean pathogens: Pseudomo- soybean strains shared a higher number of biochemical traits with nas syringae pv. glycinea, Xanthomonas axonopodis pv. glycines, P. viridiflava (Table 1) than with P. corrugata (a nonfluorescent and Curtobacterium flaccumfaciens pv. flaccumfaciens, which bacterium, positive in the oxidase test and weakly positive for cause soybean bacterial blight, soybean bacterial pustule, and bac- arginine dihydrolase activity) or with P. -
Metagenomic Characterization of Bacterial Communities on Ready-To-Eat Vegetables and Effects of Household Washing on Their Diversity and Composition
pathogens Article Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition Soultana Tatsika 1,2, Katerina Karamanoli 3, Hera Karayanni 4 and Savvas Genitsaris 1,* 1 School of Economics, Business Administration and Legal Studies, International Hellenic University, 57001 Thermi, Greece; [email protected] 2 Hellenic Food Safety Authority (EFET), 57001 Pylaia, Greece 3 School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; [email protected] 4 Department of Biological Applications and Technology, University of Ioannina, 45100 Ioannina, Greece; [email protected] * Correspondence: [email protected] Received: 8 February 2019; Accepted: 15 March 2019; Published: 19 March 2019 Abstract: Ready-to-eat (RTE) leafy salad vegetables are considered foods that can be consumed immediately at the point of sale without further treatment. The aim of the study was to investigate the bacterial community composition of RTE salads at the point of consumption and the changes in bacterial diversity and composition associated with different household washing treatments. The bacterial microbiomes of rocket and spinach leaves were examined by means of 16S rRNA gene high-throughput sequencing. Overall, 886 Operational Taxonomic Units (OTUs) were detected in the salads’ leaves. Proteobacteria was the most diverse high-level taxonomic group followed by Bacteroidetes and Firmicutes. Although they were processed at the same production facilities, rocket showed different bacterial community composition than spinach salads, mainly attributed to the different contributions of Proteobacteria and Bacteroidetes to the total OTU number. The tested household decontamination treatments proved inefficient in changing the bacterial community composition in both RTE salads. -
CAC Pests and Diseases
CAC pests and diseases A list of genus or species of fruit plant with associated pests and diseases Genus or species of fruit plant Pests Insects Cydonia, Malus, Pyrus Eriosoma lanigerum Psylla spp. Nematodes Meloidogyne hapla Meloidogyne javanica Pratylenchus penetrans Pratylenchus vulnus Fungi Armillariella mellea Chondrostereum purpureum Glomerella cingulata Pezicula alba Pezicula malicorticis Nectria galligena Phytophthora cactorum Roessleria pallida Verticillium dahlia Verticillium albo-atrum Bactreria Agrobacterium tumefaciens Pseudomonas syringae pv. syringae Viruses Cydonia and Pyrus Apple chlorotic leaf spot virus Apple stem-grooving virus Apple stem-pitting virus Virus-like diseases Bark split, bark necrosis Rough bark Rubbery wood, quince yellow blotch Viroids Pear blister canker viroid 1 Genus or species of fruit plant Pests Viruses Malus Apple chlorotic leaf spot virus Apple mosaic virus Apple stem-grooving virus Apple stem-pitting virus Virus–like diseases Rubbery wood, flat limb Horseshoe wound Fruit disorders: chat fruit, green crinkle, bumpy fruit of Ben Davis, rough skin, star crack, russet ring, russet wart Viroids Apple scar skin viroid Apple dimple fruit viroid Prunus amygdalus, P. armeniaca Insects P. domestica, P. persica and Pseudaulacaspis pentagona P. salicina Quadraspidiotus perniciosus Nematodes Meloidogyne arenaria Meloidogyne javanica Meloidogyne incognita Pratylenchus penetrans Pratylenchus vulnus Fungi Phytophthora cactorum Verticillium dahlia Bacteria Agrobacterium tumefaciens Pseudomonas syringae pv. morsprunorum Pseudomonas syringae pv. syringae (on P. armeniaca) Pseudomonas viridiflava ( on P. armeniaca) Prunus amygdalus Viruses Apple chlorotic leaf spot virus Apple mosaic virus Prune dwarf virus Prunus necrotic ringspot virus 2 Genus or species of fruit plant Pests Prunus armeniaca Viruses Apple chlorotic leaf spot virus Apple mosaic virus Apricot latent virus Prune dwarf virus Prunus necrotic ringspot virus Prunus domestica and P. -
Influence of Environment and Host Plant Genotype on the Structure And
Influence of environment and host plant genotype onthe structure and diversity of the Brassica napus seed microbiota Aude Rochefort, Martial Briand, Coralie Marais, Marie-Hélène Wagner, Anne Laperche, Patrick Vallée, Matthieu Barret, Alain Sarniguet To cite this version: Aude Rochefort, Martial Briand, Coralie Marais, Marie-Hélène Wagner, Anne Laperche, et al.. Influ- ence of environment and host plant genotype on the structure and diversity of the Brassica napus seed microbiota. Phytobiomes Journal, APS Publications, 2019, 3 (4), pp.326-336. 10.1094/PBIOMES- 06-19-0031-R. hal-02275205 HAL Id: hal-02275205 https://hal-agrocampus-ouest.archives-ouvertes.fr/hal-02275205 Submitted on 30 Aug 2019 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. Copyright Page 1 of 55 Rochefort et al., Phytobiomes Journal 1 Influence of environment and host plant genotype on the structure and 2 diversity of the Brassica napus seed microbiota 3 4 Authors and affiliations: Aude ROCHEFORT1, Martial BRIAND2, Coralie MARAIS2, Marie- 5 Hélène WAGNER3, Anne LAPERCHE1, Patrick VALLEE1, Matthieu BARRET2, Alain SARNIGUET1* 6 7 1INRA, Agrocampus-Ouest, Université de Rennes 1, UMR 1349 IGEPP (Institute of Genetics, 8 Environment and Plant Protection) – 35653 Le Rheu, France. -
Pseudomonas Viridiflava: Causal Agent of Bacterial Leaf Blight of Tomato
Pseudomonas viridiflava: Causal Agent of Bacterial Leaf Blight of Tomato J. B. JONES, Assistant Professor, and JOHN PAUL JONES, Professor, Plant Pathology, Agricultural Research and Education Center, Bradenton, FL 34203; S. M. McCARTER, Professor, Department of Plant Pathology, University of Georgia, Athens 30602; and R. E. STALL, Professor, Department of Plant Pathology, University of Florida, Gainesville 32611 ABSTRACT sprayed plants; 3)water-congested plants Jones, J. B., Jones, J. P., McCarter, S. M., and Stall, R. E. 1984. Pseudomonas viridiflava:Causal (produced by placing plants in a mist agent of bacterial leaf blight of tomato. Plant Disease 68:341-342. chamber for 6 hr before inoculation) sprayed with inoculum and held in a mist A leaf spot disease of tomato was observed in several fields near Bradenton, FL, in the late winter chamber for 36 hr; and 4) water- and early spring of 1983. A fluorescent bacterium identified as Pseudomonas viridiflava was congested plants (kept in a mist chamber isolated consistently. In controlled-environment chambers, the disease developed only when plants for 12 hr) rubbed with sterile sand bags to were water-soaked by misting before and after inoculation or where wounds were inoculated. The provide injury, then sprayed to runoff bacterium appears to be an opportunistic parasite that attacks plants stressed by unfavorable with inoculum and held for 36 hr in mist. environmental conditions. Controls were prepared using distilled water in each test. Plants were held at 20-21 C in controlled-environment Historically, bacterial spot of tomato suspension were streaked onto plates of chambers after the moisture treatments.