29 research outputs found
Combined effect of thyme and clove phenolic compounds on Xanthomonas campestris pv. campestris and biocontrol of black rot disease on cabbage seeds
The seed-borne bacterium Xanthomonas campestris pv. campestris (Xcc) as a causal organism of black rot disease remains the most serious bacterial problem of agricultural production of cruciferous plants worldwide. The eradication of a primary inoculum originating in seeds is available, but no treatment is totally effective. With the threat of developing chemical resistance and increasing pressure for sustainable disease management, biocontrol methods represent one of the main strategies currently applied in agriculture. Natural antimicrobials, including essential oils, are promising tools in disease management with low risks of environmental pollution and impact on human health. Thyme and clove essential oils were demonstrated to be highly effective in Xanthomonas studies in vitro; therefore, their application in black rot control was evaluated in this study. From five phenolic substances originating from thyme and clove essential oils (carvacrol, eugenol, linalool, p-cymene and thymol), the most promising in vitro results were observed with carvacrol, for which 0.0195% led to the death of all Xcc cells in 30 min. Moreover, a synergistic antibacterial effect of carvacrol and thymol solutions decreased the minimal inhibition concentration to 0.0049% and 0.0195% for carvacrol and thymol, respectively. Using the quadruple bactericidal values, the complete elimination of Xcc from the surface of infested cabbage seeds was obtained for both carvacrol and thymol solutions and their combined mixture at 2 MIC value. The elimination of bacterial infection from germinated cabbage plants was observed for both plate counting and quantitative real-time PCR methods. We also evaluated the effect of the application of phenolic treatment on the seed germination and germinated plants. Our results suggest a high potential of the application of carvacrol and thymol in vegetable seed production, specifically for cabbage, thus representing a suitable alternative to cupric derivatives
Cadophora sabaouae sp. nov. and Phaeoacremonium Species Associated with Petri Disease on Grapevine Propagation Material and Young Grapevines in Algeria
[EN] A field survey conducted on asymptomatic grapevine propagation material from nurseries and symptomatic young grapevines throughout different regions of Algeria yielded a collection of 70 Phaeoacremonium-like isolates and three Cadophora-like isolates. Based on morphology and DNA sequence data of I3-tubulin (tub2) and actin, five Phaeoacremonium species were identified including Phaeoacremonium minimum (22 isolates), Phaeoacremonium venezuelense (19 isolates), Phaeoacremonium parasiticum (17 isolates), Phaeoacremonium australiense (8 isolates), and Phaeoacremon bun ira nianu m (4 isolates). The latter two species (P. australiense and P. iranianum) were reported for the first time in Algeria. Multilocus phylogenetic analyses (internal transcribed spacer, tub2, and translation elongation factor 1-alpha) and morphological features, allowed the description of the three isolates belonging to the genus Cadophora (WAMC34, WAMC117, and WAMC118) as a novel species, named Cadophora sabaouae sp. nov. Pathogenicity tests were conducted on grapevine cuttings cultivar Cardinal. All the identified species were pathogenic on grapevine cuttings.This work was supported by the Ministerstvo Skolstvi, Mladeze a Telovychovy, Czech Republic under grant no. CZ-02-1-01/0-0/0-0/16-025/0007314, the Technologicka Agentura Ceske Republiky under grant no. TJ02000096, and the Spanish Government, Ramon y Cajal program under grant no. RYC-2017-23098 (to D. Gramaje).Aigoun-Mouhous, W.; Mahamedi, AE.; León Santana, M.; Chaouia, C.; Zitouni, A.; Barankova, K.; Eichmeier, A.... (2021). Cadophora sabaouae sp. nov. and Phaeoacremonium Species Associated with Petri Disease on Grapevine Propagation Material and Young Grapevines in Algeria. Plant Disease. 105(11):3657-3668. https://doi.org/10.1094/PDIS-11-20-2380-RES365736681051
Draft genome sequence of Phyllosticta ampelicida, the cause of grapevine black rot
Phyllosticta ampelicida causes grapevine black rot, a potentially damaging disease for grape production. This paper reports the draft genome sequence of P. ampelicida PA1 Galicia CBS 148563, which is 30.55 Mb and encodes 10,691 predicted protein-coding genes. This is the first sequence genome assembly of P. ampelicida, and this information is a valuable resource to support genomic attributes for determining pathogenic behaviour and comparative genomic analyses of grapevine black rot fungi
IMA genome-F18 The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1
SUPPLEMENTARY INFORMATION : Additional file 1. Table 1. Summary of genomes analysed during this
study that were correctly identified.AVAILABILITY OF DATA AND MATERIAL : Genome data for the Penicillium genomes are publicly available in the NCBI
genome database (https:// www. ncbi. nlm. nih. gov/ datas ets/ genome). The
datasets generated from Trichoderma atroviride during the current study are
available in the NCBI repository, https:// www. ncbi. nlm. nih. gov/ biopr oject/
923860. For the Penicillium species from dry cured meat the genome assembly
and annotations are available from JGI Fungal genome portal MycoCosm
under JGI Projects: 1,289,827 (ITEM 15300), 1,289,819 (ITEM 18316), 1,289,903
(ITEM 18327), and have been deposited to GenBank under BioProjects:
PRJNA970850 (ITEM 15300), PRJNA971651 (ITEM 18316), PRJNA970851
(ITEM 18327). Genome assembly and annotations are available from JGI
Fungal genome portal MycoCosm under JGI Project Id 1,289,847 and has
been deposited to GenBank under BioProject n.PRJNA971650 (BioSample n.
SAMN35051277; Project Accession n. SRP442271). The genomic sequences of
T. carnegiei have been deposited at DDJ/EMBL/GenBank under the accession
JANYMD000000000. This paper describes the first version. The genomes of the
Pewenomyces species have been deposited in the NCBI genome database.Sequencing fungal genomes has now become very common and the list of genomes in this manuscript reflects this. Particularly relevant is that the first announcement is a re-identification of Penicillium genomes available on NCBI. The fact that more than 100 of these genomes have been deposited without the correct species names speak volumes to the fact that we must continue training fungal taxonomists and the importance of the International Mycological Association (after which this journal is named). When we started the genome series in 2013, one of the essential aspects was the need to have a phylogenetic tree as part of the manuscript. This came about as the result of a discussion with colleagues in NCBI who were trying to deal with the very many incorrectly identified bacterial genomes (at the time) which had been submitted to NCBI. We are now in the same position with fungal genomes. Sequencing a fungal genome is all too easy but providing a correct species name and ensuring that the fungus has in fact been correctly identified seems to be more difficult. We know that there are thousands of fungi which have not yet been described. The availability of sequence data has made identification of fungi easier but also serves to highlight the need to have a fungal taxonomist in the project to make sure that mistakes are not made.Trichoderma atroviride SC1 genome sequencing was funded by the Ministerstvo Školství, Mládeže a Tělovýchovy and by the Internal Grant of Mendel University in Brno. The work on Penicillium species from dry cured meat is supported by the Office of Science of the U.S. Department of Energy. US Department of Energy Joint Genome Institute are supported by the Office of Science of the US Department of Energy. Funding for the project on the T. carnegiei and the Pewenomyces species genomes was provided by Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence in Plant Health Biotechnology (CPHB), South Africa and the DST-NRF SARChI chair in Fungal Genomics.https://imafungus.biomedcentral.comam2024BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyPlant Production and Soil ScienceSDG-15:Life on lan
Fungal Planet description sheets: 1182-1283
Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indoor oopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves of Stipagrostis sp., Nothophaeotheca mirabibensis (incl. Nothophaeotheca gen. nov.) on persistent inflorescence remains of Blepharis obmitrata, Paramyrothecium salvadorae on twigs of Salvadora persica, Preussia procaviicola on dung of Procavia sp., Sordaria equicola on zebra dung, Volutella salvadorae on stems of Salvadora persica. Netherlands, Entoloma ammophilum on sandy soil, Entoloma pseudocruentatum on nutrient poor(acid)soil, Entoloma pudens on plant debris, amongst grasses. [...]Leslie W.S. de Freitas and colleagues express their
gratitude to Conselho Nacional de Desenvolvimento Científico e Tecnológico
(CNPq) for scholarships provided to Leslie Freitas and for the research grant
provided to André Luiz Santiago; their contribution was financed by the
projects ‘Diversity of Mucoromycotina in the different ecosystems of the
Atlantic Rainforest of Pernambuco’ (FACEPE–First Projects Program PPP/
FACEPE/CNPq–APQ–0842-2.12/14) and ‘Biology of conservation of fungi
s.l. in areas of Atlantic Forest of Northeast Brazil’ (CNPq/ICMBio 421241/
2017-9) H.B. Lee was supported by the Graduate Program for the Undiscovered
Taxa of Korea (NIBR202130202). The study of O.V. Morozova, E.F.
Malysheva, V.F. Malysheva, I.V. Zmitrovich, and L.B. Kalinina was carried
out within the framework of a research project of the Komarov Botanical
Institute RAS (АААА-А19-119020890079-6) using equipment of its Core
Facility Centre ‘Cell and Molecular Technologies in Plant Science’. The work
of O. V. Morozova, L.B. Kalinina, T. Yu. Svetasheva, and E.A. Zvyagina was
financially supported by Russian Foundation for Basic Research project no.
20-04-00349. E.A. Zvyagina and T.Yu. Svetasheva are grateful to A.V. Alexandrova,
A.E. Kovalenko, A.S. Baykalova for the loan of specimens, T.Y.
James, E.F. Malysheva and V.F. Malysheva for sequencing. J.D. Reyes
acknowledges B. Dima for comparing the holotype sequence of Cortinarius
bonachei with the sequences in his database. A. Mateos and J.D. Reyes
acknowledge L. Quijada for reviewing the phylogeny and S. de la Peña-
Lastra and P. Alvarado for their support and help. Vladimir I. Kapitonov and
colleagues are grateful to Brigitta Kiss for help with their molecular studies.
This study was conducted under research projects of the Tobolsk Complex
Scientific Station of the Ural Branch of the Russian Academy of Sciences
(N АААА-А19-119011190112-5). E. Larsson acknowledges the Swedish
Taxonomy Initiative, SLU Artdatabanken, Uppsala (dha.2019.4.3-13). The
study of D.B. Raudabaugh and colleagues was supported by the Schmidt
Science Fellows, in partnership with the Rhodes Trust. Gregorio Delgado is
grateful to Michael Manning and Kamash Pillai (Eurofins EMLab P&K) for
provision of laboratory facilities. Jose G. Maciá-Vicente acknowledges support
from the German Research Foundation under grant MA7171/1-1, and
from the Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer
Exzellenz (LOEWE) of the state of Hesse within the framework of the Cluster
for Integrative Fungal Research (IPF). Thanks are also due to the authorities
of the Cabañeros National Park and Los Alcornocales Natural Park
for granting the collection permit and for support during field work. The study
of Alina V. Alexandrova was carried out as part of the Scientific Project of
the State Order of the Government of Russian Federation to Lomonosov
Moscow State University No. 121032300081-7. Michał Gorczak was
financially supported by the Ministry of Science and Higher Education through
the Faculty of Biology, University of Warsaw intramural grant DSM 0117600-
13. M. Gorczak acknowledges M. Klemens for sharing a photo of the
Białowieża Forest logging site and M. Senderowicz for help with preparing
the illustration. Ivona Kautmanová and D. Szabóová were funded by the
Operational Program of Research and Development and co-financed with
the European Fund for Regional Development (EFRD). ITMS 26230120004:
‘Building of research and development infrastructure for investigation of
genetic biodiversity of organisms and joining IBOL initiative’. Ishika Bera,
Aniket Ghosh, Jorinde Nuytinck and Annemieke Verbeken are grateful to the
Director, Botanical Survey of India (Kolkata), Head of the Department of
Botany & Microbiology & USIC Dept. HNB Garhwal University, Srinagar,
Garhwal for providing research facilities. Ishika Bera and Aniket Ghosh acknowledge
the staff of the forest department of Arunachal Pradesh for facilitating
the macrofungal surveys to the restricted areas. Sergey Volobuev
was supported by the Russian Science Foundation (RSF project N 19-77-
00085). Aleksey V. Kachalkin and colleagues were supported by the Russian
Science Foundation (grant No. 19-74-10002). The study of Anna M.
Glushakova was carried out as part of the Scientific Project of the State
Order of the Government of Russian Federation to Lomonosov Moscow
State University No. 121040800174-6. Tracey V. Steinrucken and colleagues
were supported by AgriFutures Australia (Rural Industries Research and
Development Corporation), through funding from the Australian Government
Department of Agriculture, Water and the Environment, as part of its Rural
Research and Development for Profit program (PRJ-010527). Neven Matočec
and colleagues thank the Croatian Science Foundation for their financial
support under the project grant HRZZ-IP-2018-01-1736 (ForFungiDNA). Ana
Pošta thanks the Croatian Science Foundation for their support under the
grant HRZZ-2018-09-7081. The research of Milan Spetik and co-authors
was supported by Internal Grant of Mendel University in Brno No. IGAZF/
2021-SI1003. K.C. Rajeshkumar thanks SERB, the Department of Science
and Technology, Government of India for providing financial support
under the project CRG/2020/000668 and the Director, Agharkar Research
Institute for providing research facilities. Nikhil Ashtekar thanks CSIR-HRDG,
INDIA, for financial support under the SRF fellowship (09/670(0090)/2020-EMRI),
and acknowledges the support of the DIC Microscopy Facility, established
by Dr Karthick Balasubramanian, B&P (Plants) Group, ARI, Pune. The research
of Alla Eddine Mahamedi and co-authors was supported by project
No. CZ.02.1.01/0.0/0.0/16_017/0002334, Czech Republic. Tereza Tejklová
is thanked for providing useful literature. A. Polhorský and colleagues were
supported by the Operational Program of Research and Development and
co-financed with the European fund for Regional Development (EFRD), ITMS
26230120004: Building of research and development infrastructure for investigation
of genetic biodiversity of organisms and joining IBOL initiative.
Yu Pei Tan and colleagues thank R. Chen for her technical support. Ernest
Lacey thanks the Cooperative Research Centres Projects scheme (CRCPFIVE000119)
for its support. Suchada Mongkolsamrit and colleagues were
financially supported by the Platform Technology Management Section,
National Center for Genetic Engineering and Biotechnology (BIOTEC),
Project Grant No. P19-50231. Dilnora Gouliamova and colleagues were
supported by a grant from the Bulgarian Science Fund (KP-06-H31/19). The
research of Timofey A. Pankratov was supported by the Russian Foundation
for Basic Research (grant No. 19-04-00297a). Gabriel Moreno and colleagues
wish to express their gratitude to L. Monje and A. Pueblas of the Department
of Drawing and Scientific Photography at the University of Alcalá for their
help in the digital preparation of the photographs, and to J. Rejos, curator of
the AH herbarium, for his assistance with the specimens examined in the
present study. Vit Hubka was supported by the Charles University Research
Centre program No. 204069. Alena Kubátová was supported by The National
Programme on Conservation and Utilization of Microbial Genetic
Resources Important for Agriculture (Ministry of Agriculture of the Czech
Republic). The Kits van Waveren Foundation (Rijksherbariumfonds Dr E. Kits
van Waveren, Leiden, Netherlands) contributed substantially to the costs of
sequencing and travelling expenses for M. Noordeloos. The work of B. Dima
was supported by the ÚNKP-20-4 New National Excellence Program of the
Ministry for Innovation and Technology from the source of the National Research,
Development and Innovation Fund, and by the ELTE Thematic Excellence
Programme 2020 supported by the National Research, Development
and Innovation Office of Hungary (TKP2020-IKA-05). The Norwegian Entoloma
studies received funding from the Norwegian Biodiversity Information
Centre (NBIC), and the material was partly sequenced through NorBOL.
Gunnhild Marthinsen and Katriina Bendiksen (Natural History Museum,
University of Oslo, Norway) are acknowledged for performing the main parts
of the Entoloma barcoding work. Asunción Morte is grateful to AEI/FEDER,
UE (CGL2016-78946-R) and Fundación Séneca - Agencia de Ciencia y
Tecnología de la Región de Murcia (20866/PI/18) for financial support.
Vladimír Ostrý was supported by the Ministry of Health, Czech Republic -
conceptual development of research organization (National Institute of
Public Health – NIPH, IN 75010330). Konstanze Bensch (Westerdijk Fungal
Biodiversity Institute, Utrecht) is thanked for correcting the spelling of various
Latin epithets.Peer reviewe
Conserved MicroRNAs in Human Nasopharynx Tissue Samples from Swabs Are Differentially Expressed in Response to SARS-CoV-2
The use of high-throughput small RNA sequencing is well established as a technique to unveil the miRNAs in various tissues. The miRNA profiles are different between infected and non-infected tissues. We compare the SARS-CoV-2 positive and SARS-CoV-2 negative RNA samples extracted from human nasopharynx tissue samples to show different miRNA profiles. We explored differentially expressed miRNAs in response to SARS-CoV-2 in the RNA extracted from nasopharynx tissues of 10 SARS-CoV-2-positive and 10 SARS-CoV-2-negative patients. miRNAs were identified by small RNA sequencing, and the expression levels of selected miRNAs were validated by real-time RT-PCR. We identified 943 conserved miRNAs, likely generated through posttranscriptional modifications. The identified miRNAs were expressed in both RNA groups, NegS and PosS: miR-148a, miR-21, miR-34c, miR-34b, and miR-342. The most differentially expressed miRNA was miR-21, which is likely closely linked to the presence of SARS-CoV-2 in nasopharynx tissues. Our results contribute to further understanding the role of miRNAs in SARS-CoV-2 pathogenesis, which may be crucial for understanding disease symptom development in humans
Effect of hot-water treatment on grapevine viability and fungal trunk diseases pathogens diversity by RNA high-throughput amplicon sequencing
Trabajo presentado en el 12th International Workshop on Grapevine Trunk Diseases, celebrado en Mikulov (República Checa), del 10 al 14 de julio de 2022Effects of hot-water treatment (HWT) on grapevine
fungal communities have been mostly studied using
culture dependent methods. Changes in potentially
active fungal communities of grapevine wood were
assessed after application of two HWT protocols (50ºC
for 45 min, or 53ºC for 30 min), using RNA high
throughput amplicon sequencing (HTAS) for several
cultivar/rootstock combinations during two years. Fungal diversity was only reduced by both HWT protocols
during the second year of study. The effects of HWT on
grapevine trunk disease (GTD) pathogen abundance
varied, according to the fungal genera and the HWT
protocol. In some cases, HWT increased the abundance
of GTD fungi (i.e. Diaporthe), but in other cases, GTD
abundances decreased after HWT (i.e. Dothiorella). To
evaluate the viability of planting material, treated plants
were planted in a vineyard immediately after HWT, or
1, 2 or 3 months after treatments. Grapevine viability
was high 1 month after treatment, but decreased as time
from HWT to vineyard establishment increased. Plants
established 3 months after treatments were less than
90% viable over 30% of combinations in the first year,
and over more than 50% of combinations were affected
in the second yea