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Wei TT, Fan XB, Quan ZX. Abyssibius alkaniclasticus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae, isolated from the Mariana Trench. Int J Syst Evol Microbiol 2023; 73. [PMID: 36790414 DOI: 10.1099/ijsem.0.005715] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
A Gram-stain-negative bacterium with rod-shaped or irregular cells approximately 0.5-0.9×2.0-3.8 µm in size, designated as 960558T, was isolated from sediment sampled in the Mariana Trench. Strain 960558T grows at 4-37 °C (optimum, 28 °C), pH 6-7 (optimum, pH 7) and in the presence of 1-5 % (w/v) NaCl (optimum, 3 %). Strain 960558T utilizes tetradecane or hexadecane as a sole carbon and energy source, respectively. Phylogenetic trees based on 16S rRNA gene sequences and phylogenomic reconstruction revealed a close phylogenetic relationship between strain 960558T and members of the family Rhodobacteraceae by forming a separate branch within the type species of closely related genera. The validly published species that is most closely related to strain 960558T is Planktotalea lamellibrachiae JAM 119T, which has the highest 16S rRNA gene sequence similarity (93.47 %). Ubiquinone 10 is the predominant ubiquinone, while C16 : 0, 11-methyl C18 : 1 ω7c and C18 : 1 ω7c and/or C18 : 1 ω6c are the predominant fatty acids (>10 %). Additionally, phosphatidylglycerol, glycolipids, diphosphatidylglycerol, unidentified polar lipids and unidentified aminolipids are the major polar lipids. The DNA G+C content of strain 960558T is 61 %. Average nucleotide identity and digital DNA-DNA hybridization results of strain 960558T with other type strains are <70.2 and 22.1 %, respectively. Based on its phylogenetic, chemotaxonomic and other phenotypic properties, strain 960558T is considered to represent a novel genus and species within the family Rhodobacteraceae, for which the name Abyssibius alkaniclasticus gen. nov., sp. nov. is proposed. The type strain of Abyssibius alkaniclasticus is 960558T (=KCTC 82619T=MCCC 1K04727T).
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Affiliation(s)
- Ting-Ting Wei
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Xi-Bei Fan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, PR China
- Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, PR China
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202
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Uyar E, Avcı T. Screening and molecular identification of biosurfactant/bioemulsifier producing bacteria from crude oil contaminated soils samples. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01330-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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203
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Gupta MK, Vadde R. Next-generation development and application of codon model in evolution. Front Genet 2023; 14:1091575. [PMID: 36777719 PMCID: PMC9911445 DOI: 10.3389/fgene.2023.1091575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine.
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204
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Berto BP, Machado EL, Hossotani CMDS, Beretta BMS, da Silva DRR, Nakamura AA, Meireles MV. Integrative taxonomy for the traditional coccidians (Chromista: Miozoa: Eimeriidae) from island canaries (Aves: Passeriformes: Fringillidae): Worldwide distribution, morphological and molecular characterization, revaluations and establishment of junior synonyms. Syst Parasitol 2023; 100:245-259. [PMID: 36701030 DOI: 10.1007/s11230-023-10084-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/06/2023] [Indexed: 01/27/2023]
Abstract
Island canaries Serinus canaria (Linnaeus) are finches native to the North Atlantic Islands, however, they have a worldwide distribution in captivity due to their relevance as a pet bird. Coccidians are the most reported parasites of passerines worldwide, both in the wild and in captivity, being frequently associated with disease in passerines kept in rehabilitation centers and commercial breeders. This study aimed to identify coccidians from island canaries kept in captivity in Brazil. Three hundred and fifteen genomic DNA extracted from fecal samples of island canaries from different breeders from Southern and Southeastern Brazil were used to perform a nested PCR assay to amplify a partial fragment of the 28S small subunit ribosomal RNA gene (28S) of Isospora spp. Microscopic screening and morphological identification of Isospora oocysts was performed in fecal samples corresponding to PCR positive DNA samples. Fecal samples have been formalin-stored for approximately four years. Positivity rate for both microscopy and PCR was 10.5% (33/315). Posteriorly, Isospora serini (Aragão, 1933) Box, 1975 and Isospora canaria Box, 1975 were morphologically identified from fresh fecal samples of island canaries maintained by a breeder in the State of São Paulo, Southeastern Brazil, providing a genotypic characterization via sequencing of the mitochondrial cytochrome c oxidase subunit 1 (COI) and 28S genes. The 28S and COI sequences referring to the morphological identification of I. canaria was, respectively, 100% and 99% similar to sequences deposited as Isospora serinuse Yang, Brice, Elliot & Ryan, 2015 from island canaries kept in a rehabilitation center in Australia. The COI sequence referring to the morphological identification of I. serini was 100% similar to a sequence of an extraintestinal Isospora, corroborating this identification/sequencing since I. serini is the first isosporan with an extra-intestinal cycle demonstrated. The comparison of morphological and molecular data from I. canaria and I. serini from this study with published data of Isospora spp. from canaries worldwide, allowed the specific identification from preliminary generic identifications, correction of misidentifications, as well as the establishment of junior synonyms. Finally, this study provides morphological and molecular data that ensure the correct identification of the two Isospora spp. from island canaries in future studies worldwide.
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Affiliation(s)
- Bruno Pereira Berto
- Departamento de Biologia Animal, Instituto de Ciências Biológicas e da Saúde, Universidade Federal Rural do Rio de Janeiro, BR-465 km 7, Seropédica, Rio de Janeiro, 23897-000, Brazil.
| | - Evelyn Lina Machado
- Faculdade de Medicina Veterinária, Universidade Estadual Paulista, Rua Clóvis Pestana 793, Araçatuba, São Paulo, 16050-680, Brazil
| | | | - Bruna Matarucco Sampaio Beretta
- Faculdade de Medicina Veterinária, Universidade Estadual Paulista, Rua Clóvis Pestana 793, Araçatuba, São Paulo, 16050-680, Brazil
| | - Débora Regina Romualdo da Silva
- Faculdade de Medicina Veterinária, Universidade Estadual Paulista, Rua Clóvis Pestana 793, Araçatuba, São Paulo, 16050-680, Brazil
| | - Alex Akira Nakamura
- Faculdade de Medicina Veterinária, Universidade Estadual Paulista, Rua Clóvis Pestana 793, Araçatuba, São Paulo, 16050-680, Brazil
| | - Marcelo Vasconcelos Meireles
- Faculdade de Medicina Veterinária, Universidade Estadual Paulista, Rua Clóvis Pestana 793, Araçatuba, São Paulo, 16050-680, Brazil.
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205
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Didyk YM, Mangová B, Špitalská E, Derdáková M. Rickettsial infection in Ixodes ricinus and Dermacentor reticulatus ticks in urban green areas of Ukraine. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01323-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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206
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A novel nitrogen-fixing bacterium, Propionivibrio soli sp. nov. isolated from paddy soil. Arch Microbiol 2023; 205:68. [PMID: 36662302 DOI: 10.1007/s00203-023-03413-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/21/2023]
Abstract
A facultative anaerobic nitrogen-fixing bacterium, designated SG131T, was isolated from paddy soil. Strain SG131T showed high 16S rRNA gene sequence similarities with type strains Propionivibrio limicola DSM 6832T (96.9%), Propionivibrio pelophilus asp 66T (96.0%) and Propionivibrio dicarboxylicus DSM 5885T (95.7%). The phylogenetic trees (based on 16S rRNA gene sequences and 120 conserved genes from genomes, respectively) indicated that strain SG131T clustered with members of the genus Propionivibrio. Growth of strain SG131T was observed at 25-40 °C, pH 5.5-10.5 and 0-0.5% (w/v) NaCl. The quinone was Q-7, and the main fatty acids were C16:1 ω6c and/or C16:1 ω7c (25.9%), C16:0 (23.3%), C17:0-cyclo (11.7%), C12:0 (6.0%) and C17:0 (5.9%). The genomic DNA G + C content of strain SG131T was 60.3%. The average nucleotide identity (ANI) values between strain SG131T and its most closely related species P. limicola DSM 6832T, P. pelophilus DSM 12018T and P. dicarboxylicus DSM 5885T were 74.4%, 74.9% and 75.6%, respectively. The digital DNA-DNA hybridization (dDDH) values between strain SG131T and its most closely related species P. limicola DSM 6832T, P. pelophilus DSM 12018T and P. dicarboxylicus DSM 5885T were 19.9%, 20.6% and 20.5%, respectively. All these values were lower than the recommended species delineation thresholds of ANI (95-96%) and dDDH (70%). Strain SG131T possessed core genes (nifHDK) of nitrogen fixation and was confirmed its nitrogen-fixing ability by the ARA method. According to the above-described analysis, strain SG131T represents a novel species of the genus Propionivibrio, for which the name Propionivibrio soli sp. nov. is proposed. The type strain is SG131T (= GDMCC 1.3313T = JCM 35595T).
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207
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Andreou A, Papakyriakou A, Zervou MI, Goulielmos GN, Eliopoulos EE. Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics? J Mol Evol 2023; 91:204-213. [PMID: 36651965 PMCID: PMC10082101 DOI: 10.1007/s00239-022-10090-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/27/2022] [Indexed: 01/19/2023]
Abstract
Interferon induced with helicase C domain-containing protein 1 (IFIH1) gene encodes a cytoplasmic RNA helicase otherwise known as melanoma differentiation-associated 5 (MDA5), a RIG-1-like RNA helicase that recognizes viral RNA and is involved in innate immunity through recognition of viral RNA. Upon binding to double-stranded (ds) RNA, MDA5 forms a filamentous assembly along the length of dsRNA and utilizes molecular signatures to discriminate self, versus non-self on the basis of dsRNA length and methylation. Its missense variant rs35667974 is protective for type 1 diabetes, psoriasis, and psoriatic arthritis, but is also found to be associated with an increased risk for ankylosing spondylitis, Crohn's disease, and ulcerative colitis. To gain insight into the complex role of this variant we performed a structural analysis of MDA5 in complex with dsRNA using molecular dynamics simulations. Our data suggest that while the Ile923Val mutation of the rs35667974 variant does not affect binding to native dsRNA significantly, it displays a destabilizing effect in the presence of 2'-O uridine methylation. Thus, the presence of 2'-O-methylation at the dsRNA introduces a sensing signature that leads to selective reduction of the overall MDA catalytic activity. This study represents an evaluation of the role of the shared rs35667974 variant of autoimmune locus IFIH1, reported to lead to selectively reduced catalytic activity of the modified MDA5 phenotype and, as a consequence, reduced negative feedback on cytokine and chemokine signaling and selectively protection against autoimmunity.
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Affiliation(s)
- Athena Andreou
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", 15341, Athens, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003, Heraklion, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003, Heraklion, Greece.,Department of Internal Medicine, University Hospital of Heraklion, 71500, Heraklion, Greece
| | - Elias E Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855, Athens, Greece.
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208
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Heino MT, Nyman T, Palo JU, Harmoinen J, Valtonen M, Pilot M, Översti S, Salmela E, Kunnasranta M, Väinölä R, Hoelzel AR, Aspi J. Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections. Ecol Evol 2023; 13:e9720. [PMID: 36699566 PMCID: PMC9849707 DOI: 10.1002/ece3.9720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/20/2023] Open
Abstract
The Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to postglacial bedrock rebound around 9000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. We sequenced sections of the mitochondrial control region from 60 up to 125-years-old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies and how it is phylogenetically related to other ringed seal populations from the Baltic Sea, Lake Ladoga, North America, Svalbard, and the White Sea. We observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation also shows affinities to North American ringed seals. Our results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seal is not representative of the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.
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Affiliation(s)
- Matti T. Heino
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland,Department of Forensic MedicineUniversity of HelsinkiHelsinkiFinland
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Jukka U. Palo
- Department of Forensic MedicineUniversity of HelsinkiHelsinkiFinland,Forensic Chemistry Unit/Forensic GeneticsFinnish Institute for Health and WelfareHelsinkiFinland
| | - Jenni Harmoinen
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland,Wildlife Ecology GroupNatural Resources Institute FinlandHelsinkiFinland
| | - Mia Valtonen
- Wildlife Ecology GroupNatural Resources Institute FinlandHelsinkiFinland,Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland,Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | - Małgorzata Pilot
- School of Biological and Biomedical SciencesDurham UniversityDurhamUK,Museum and Institute of ZoologyPolish Academy of SciencesGdańskPoland,Faculty of BiologyUniversity of GdańskGdańskPoland
| | - Sanni Översti
- Transmission, Infection, Diversification and Evolution GroupMax‐Planck Institute for the Science of Human HistoryJenaGermany,Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Elina Salmela
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland,Department of Biology, Faculty of ScienceUniversity of TurkuTurkuFinland
| | - Mervi Kunnasranta
- University of Eastern FinlandJoensuuFinland,Natural Resources Institute FinlandJoensuuFinland
| | - Risto Väinölä
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | | | - Jouni Aspi
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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209
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Requena E, Alonso-Guirado L, Veloso J, Villarino M, Melgarejo P, Espeso EA, Larena I. Comparative analysis of Penicillium genomes reveals the absence of a specific genetic basis for biocontrol in Penicillium rubens strain 212. Front Microbiol 2023; 13:1075327. [PMID: 36713150 PMCID: PMC9880469 DOI: 10.3389/fmicb.2022.1075327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/06/2022] [Indexed: 01/15/2023] Open
Abstract
Penicillium rubens strain 212 (PO212) is a filamentous fungus belonging to the division Ascomycete. PO212 acts as an effective biocontrol agent against several pathogens in a variety of horticultural crops including Fusarium oxysporum f.sp. lycopersici, causing vascular wilt disease in tomato plants. We assembled draft genomes of two P. rubens strains, the biocontrol agent PO212 and the soil isolate S27, which lacks biocontrol activity. We also performed comparative analyses of the genomic sequence of PO212 with that of the other P. rubens and P. chrysogenum strains. This is the first Penicillium strain with biocontrol activity whose genome has been sequenced and compared. PO212 genome size is 2,982 Mb, which is currently organized into 65 scaffolds and a total of 10,164 predicted Open Reading Frames (ORFs). Sequencing confirmed that PO212 belongs to P. rubens clade. The comparative analysis of the PO212 genome with the genomes of other P. rubens and Penicillium chrysogenum strains available in databases showed strong conservation among genomes, but a correlation was not found between these genomic data and the biocontrol phenotype displayed by PO212. Finally, the comparative analysis between PO212 and S27 genomes showed high sequence conservation and a low number of variations mainly located in ORF regions. These differences found in coding regions between PO212 and S27 genomes can explain neither the biocontrol activity of PO212 nor the absence of such activity in S27, opening a possible avenue toward transcriptomic and epigenetic studies that may shed light on this mechanism for fighting plant diseases caused by fungal pathogens. The genome sequences described in this study provide a useful novel resource for future research into the biology, ecology, and evolution of biological control agents.
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Affiliation(s)
- Elena Requena
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain
| | - Lola Alonso-Guirado
- Grupo de Epidemiología Genética y Molecular, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Javier Veloso
- Departamento de Biología Funcional, Escuela Politécnica Superior de Ingeniería, Universidad de Santiago de Compostela, Lugo, Spain
| | - María Villarino
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain
| | - Paloma Melgarejo
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain
| | - Eduardo Antonio Espeso
- Laboratorio de Biología Celular de Aspergillus, Departamento de Biología Celular y Molecular, Centro de Investigaciones Biológicas Margarita Salas, CSIC (CIB-CSIC), Madrid, Spain
| | - Inmaculada Larena
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain,*Correspondence: Inmaculada Larena, ✉
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210
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Ali A, Umar UUD, Naqvi SAH, Shakeel MT, Tahir MN, Khan MF, Altaf MT, Ölmez F, Dababat AA, Haq ZU, Nadeem MA, Hatipoğlu R, Baloch FS, Chung YS. Molecular characterization of divergent isolates of Citrus bent leaf viroid (CBLVd) from citrus cultivars of Punjab, Pakistan. Front Genet 2023; 13:1104635. [PMID: 36712883 PMCID: PMC9878587 DOI: 10.3389/fgene.2022.1104635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Citrus viroid infection is emerging as a serious threat because of its efficient systemic movement within the host plant and its quick spread due to contaminated pruning tools. A survey was conducted to investigate the primary distribution and molecular characterization of Citrus bent leaf viroid (CBLVd) and its variants in different citrus cultivars. A total of 154 symptomatic citrus samples were collected and detected by RT‒PCR with newly designed specific primers with the incidence of 36.33%. During biological indexing study on Etrog citron, expressions of reduced leaf size, yellowing with a light green pattern, and bending were observed. Amplified products were sequenced and analyzed using a nucleotide BLAST search, which showed 98% homology with other CBLVd isolates. The results of the phylogenetic tree analysis showed the presence of two main groups (A and B), with the predominant variants of CBLVd, i.e., CVd-I-LSS (Citrus viroid Low Sequence Similarity) sequences, clustering in subgroup A1 along with newly detected CVd-I-LSS from Palestinian sweet lime (Citrus limettioides), which has been identified as a new host of CVd-I-LSS in Pakistan. Further analysis of the sequences in subgroup A1 showed that the variant of CVd-I-LSS infecting citrus cultivars had a close relationship with isolates reported from China, Japan, and Iran, which may have resulted from the exchange of planting material. This study also unveiled the variability in nucleotide sequences of CBLVd, which made it unable to be detected by old primers. The results of this study indicate that the widespread presence of divergent variants of CBLVd is a major concern for the citrus industry in Pakistan and other countries where virulent isolates of CBLVd are prevalent. These findings suggest the need for future research on effective management and quarantine measures to stop the spread of CBLVd.
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Affiliation(s)
- Amjad Ali
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan,Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | - Ummad ud Din Umar
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan,*Correspondence: Ummad ud Din Umar, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Syed Atif Hasan Naqvi
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan
| | | | - Muhammad Nouman Tahir
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera GhaziKhan, Punjab, Pakistan
| | - Muhammad Fahad Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera GhaziKhan, Punjab, Pakistan
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | - Fatih Ölmez
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | | | - Zia ul Haq
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, BahauddinZakariya University, Multan, Punjab, Pakistan
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, Kirsehir Ahi Evran Universitesi, Kirsehir, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, Sivas University of Science and Technology, Sivas, Turkey,*Correspondence: Ummad ud Din Umar, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yong Suk Chung
- Department of Field Crops, Faculty of Agriculture, Kirsehir Ahi Evran Universitesi, Kirsehir, Turkey,*Correspondence: Ummad ud Din Umar, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
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211
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A recent view about encephalomyocarditis virus circulating in compartmentalised animal population in Northern Italy. Sci Rep 2023; 13:592. [PMID: 36631510 PMCID: PMC9834260 DOI: 10.1038/s41598-023-27828-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Encephalomyocarditis virus (Picornaviridae, Cardiovirus A) is the causative agent of the homonymous disease, which may induce myocarditis, encephalitis and reproductive disorders in various mammals, especially in swine. Despite the disease occurred endemically in pig farms since 1997, the recent increase of death experimented in Northern Italy prompted to furtherly investigate the evolution of the virus and the actual spread of the infection. Italian EMC viruses, collected between 2013 and 2019, showed an overall antigenic stability. The in-house ELISA Monoclonal Antibodies based, able to reveal changes in seven different antigenic sites, showed only sporadic and occasional mutations in considered samples and the subsequent phylogenetic analysis confirmed antigenic panel's remarks. All the isolates could be classified within a unique lineage, which comprise other European strains and confirm that the viruses currently circulating in Italy developed from a unique common ancestor. Despite the demonstrated stability of virus, some putative newly emerged variants were detected through antigenic profile analysis and phylogenesis. Finally, the serosurvey proved that spread of EMCV is greater than the diffusion of fatal infections would suggest, due to subclinical circulation of EMCV. It demonstrated an increase in the proportion of seropositive farms, if compared with previous data with no remarkable differences between farms with and without clinical evidence of disease.
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212
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Gohar IMA, Alyamani A, Shafi ME, Mohamed EAE, Ghareeb RY, Desoky EM, Hasan ME, Zaitoun AF, Abdelsalam NR, El-Tarabily KA, Elnahal ASM. A quantitative and qualitative assessment of sugar beet genotype resistance to root-knot nematode, Meloidogyne incognita. FRONTIERS IN PLANT SCIENCE 2023; 13:966377. [PMID: 36714787 PMCID: PMC9881751 DOI: 10.3389/fpls.2022.966377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/28/2022] [Indexed: 06/18/2023]
Abstract
Sugar beet productivity is highly constrained by the root-knot nematode (RKN) Meloidogyne incognita. Eight sugar beet genotypes were screened under greenhouse conditions for their susceptibility to M. incognita according to an adapted quantitative scheme for assignment Canto-Saenz's host suitability (resistance) designations (AQSCS). Besides, the degree of susceptibility or tolerance of the examined genotypes was recorded by the modified host-parasite index (MHPI) scale based on yield performance. In addition, single nucleotide polymorphism (SNP) was also determined. Sugar beet genotypes have been classified into four categories for their susceptibility or tolerance according to the AQSCS scale. The first category, the moderately resistant (MR) group implies only one variety named SVH 2015, which did not support nematode reproduction (RF≤1), and had less root damage (GI≈2). Second, the tolerant group (T) involving Lilly and Halawa KWS supported fairly high nematode reproduction (RF>1) with relatively plant damage (GI≤2). Whereas the susceptible (S) category involved four varieties, FARIDA, Lammia KWS, Polat, and Capella, which supported nematode reproduction factor (RF>1) with high plant damage (GI>2). The fourth category refers to the highly susceptible (HYS) varieties such as Natura KWS that showed (RF≤1) and very high plant damage (GI>2). However, the MHPI scale showed that Lammia KWS variety was shifted from the (S) category to the (T) category. Results revealed significant differences among genotypes regarding disease severity, yield production, and quality traits. The SVH 2015 variety exhibited the lowest disease index values concerning population density with 800/250 cm3 soils, RF=2, root damage/gall index (GI=1.8), gall size (GS=2.3), gall area (GA=3.7), damage index (DI=3.4), susceptibility rate (SR=2.4), and MHP index (MHPI=2.5). However, Lammia KWS showed the highest disease index values regarding population density with 8890/250 cm3 soils, RF= 22.2, GI= 4.8, and SR= 14.1. Meanwhile, Natura KWS the highest GS, GA and MHPI with 7.1, 8 and 20.9, respectively. The lowest DI was achieved by Capella (DI= 6) followed by Lammia KWS (DI= 5.9). For yield production, and quality traits, SVH 2015 exhibited the lowest reductions of sugar yields/beet's root with 11.1%. While Natura KWS had the highest reduction with 79.3%, as well as it showed the highest reduction in quality traits; including sucrose, T.S.S, and purity with 65, 27.3, and 51.9%, respectively. The amino acid alignment and prediction of the DNA sequences revealed the presence of five SNPs among all sugar beet verities.
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Affiliation(s)
- Ibrahim M. A. Gohar
- Sugar Crops Research Institute, Department of Sugar Crops Disease and Pests Research, Agricultural Research Center, Giza, Egypt
| | - Amal Alyamani
- Department of Biotechnology, Faculty of Sciences, Taif University, Taif, Saudi Arabia
| | - Manal E. Shafi
- Department of Biological Sciences, Zoology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Elshaimaa A. E. Mohamed
- Sugar Crops Research Institute, Department of Genetic and Breeding, Agricultural Research Center, Giza, Egypt
| | - Rehab Y. Ghareeb
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, The City of Scientific Research and Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Elsayed M. Desoky
- Botany Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Mohamed E. Hasan
- Bioinformatic Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Amera F. Zaitoun
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Nader R. Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Khaled A. El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Ahmed S. M. Elnahal
- Plant Pathology Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
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Strejčková B, Mazzucotelli E, Čegan R, Milec Z, Brus J, Çakır E, Mastrangelo AM, Özkan H, Šafář J. Wild emmer wheat, the progenitor of modern bread wheat, exhibits great diversity in the VERNALIZATION1 gene. FRONTIERS IN PLANT SCIENCE 2023; 13:1106164. [PMID: 36684759 PMCID: PMC9853909 DOI: 10.3389/fpls.2022.1106164] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Wild emmer wheat is an excellent reservoir of genetic variability that can be utilized to improve cultivated wheat to address the challenges of the expanding world population and climate change. Bearing this in mind, we have collected a panel of 263 wild emmer wheat (WEW) genotypes across the Fertile Crescent. The genotypes were grown in different locations and phenotyped for heading date. Genome-wide association mapping (GWAS) was carried out, and 16 SNPs were associated with the heading date. As the flowering time is controlled by photoperiod and vernalization, we sequenced the VRN1 gene, the most important of the vernalization response genes, to discover new alleles. Unlike most earlier attempts, which characterized known VRN1 alleles according to a partial promoter or intron sequences, we obtained full-length sequences of VRN-A1 and VRN-B1 genes in a panel of 95 wild emmer wheat from the Fertile Crescent and uncovered a significant sequence variation. Phylogenetic analysis of VRN-A1 and VRN-B1 haplotypes revealed their evolutionary relationships and geographic distribution in the Fertile Crescent region. The newly described alleles represent an attractive resource for durum and bread wheat improvement programs.
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Affiliation(s)
- Beáta Strejčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) Research Centre for Genomics and Bioinformatics via San Protaso 302, Fiorenzuola d’Arda, Italy
| | - Radim Čegan
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, ;Czechia
| | - Zbyněk Milec
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Esra Çakır
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics (CREA) Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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214
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Bahri BA, Parvathaneni RK, Spratling WT, Saxena H, Sapkota S, Raymer PL, Martinez-Espinoza AD. Whole genome sequencing of Clarireedia aff. paspali reveals potential pathogenesis factors in Clarireedia species, causal agents of dollar spot in turfgrass. Front Genet 2023; 13:1033437. [PMID: 36685867 PMCID: PMC9849252 DOI: 10.3389/fgene.2022.1033437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/21/2022] [Indexed: 01/06/2023] Open
Abstract
Dollar spot is one of the most damaging diseases in turfgrass, reducing its quality and playability. Two species, Clarireedia monteithiana and C. jacksonii (formerly Sclerotinia homoeocarpa) have been reported so far in the United States To study the Clarireedia genome, two isolates H2 and H3, sampled from seashore paspalum in Hawaii in 2019 were sequenced via Illumina paired-end sequencing by synthesis technology and PacBio SMRT sequencing. Both isolates were identified as C. aff. paspali, a novel species in the United States Using short and long reads, C. aff. paspali H3 contained 193 contigs with 48.6 Mbp and presented the most completed assembly and annotation among Clarireedia species. Out of the 13,428 protein models from AUGUSTUS, 349 cytoplasmic effectors and 13 apoplastic effectors were identified by EffectorP. To further decipher Clarireedia pathogenicity, C. aff. paspali genomes (H2 and H3), as well as available C. jacksonii (LWC-10 and HRI11), C. monteithiana (DRR09 and RB-19) genomes were screened for fifty-four pathogenesis determinants, previously identified in S. sclerotiorum. Seventeen orthologs of pathogenicity genes have been identified in Clarireedia species involved in oxalic acid production (pac1, nox1), mitogen-activated protein kinase cascade (pka1, smk3, ste12), appressorium formation (caf1, pks13, ams2, rgb1, rhs1) and glycolytic pathway (gpd). Within these genes, 366 species-specific SNPs were recorded between Clarireedia species; twenty-eight were non-synonymous and non-conservative. The predicted protein structure of six of these genes showed superimposition of the models among Clarireedia spp. The genomic variations revealed here could potentially lead to differences in pathogenesis and other physiological functions among Clarireedia species.
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Affiliation(s)
- Bochra Amina Bahri
- Department of Plant Pathology, University of Georgia, Griffin, GA, United States,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, United States,*Correspondence: Bochra Amina Bahri,
| | - Rajiv Krishna Parvathaneni
- Department of Plant Pathology, University of Georgia, Griffin, GA, United States,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, United States
| | | | - Harshita Saxena
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, United States
| | - Suraj Sapkota
- Department of Plant Pathology, University of Georgia, Griffin, GA, United States
| | - Paul L. Raymer
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, United States,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
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215
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Alburaki M, Madella S, Lopez J, Bouga M, Chen Y, vanEngelsdorp D. Honey bee populations of the USA display restrictions in their mtDNA haplotype diversity. Front Genet 2023; 13:1092121. [PMID: 36685818 PMCID: PMC9845583 DOI: 10.3389/fgene.2022.1092121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023] Open
Abstract
The genetic diversity of the USA honey bee (Apis mellifera L.) populations was examined through a molecular approach using two mitochondrial DNA (mtDNA) markers. A total of 1,063 samples were analyzed for the mtDNA intergenic region located between the cytochrome c oxidase I and II (COI-COII) and 401 samples were investigated for the NADH dehydrogenase 2 (ND2) coding gene. The samples represented 45 states, the District of Colombia and two territories of the USA. Nationwide, three maternal evolutionary lineages were identified: the North Mediterranean lineage C (93.79%), the West Mediterranean lineage M (3.2%) and the African lineage A (3.01%). A total of 27 haplotypes were identified, 13 of them (95.11%) were already reported and 14 others (4.87%) were found to be novel haplotypes exclusive to the USA. The number of haplotypes per state/territory ranged between two and eight and the haplotype diversity H ranged between 0.236-0.763, with a nationwide haplotype diversity of 0.597. Furthermore, the honey bee populations of the USA were shown to rely heavily (76.64%) on two single haplotypes (C1 = 38.76%, C2j = 37.62%) of the same lineage characterizing A. m. ligustica and A. m. carnica subspecies, respectively. Molecular-variance parsimony in COI-COII and ND2 confirmed this finding and underlined the central and ancestral position of C2d within the C lineage. Moreover, major haplotypes of A. m. mellifera (M3a, M7b, M7c) were recorded in six states (AL, AR, HI, MO, NM and WA). Four classic African haplotypes (A1e, A1v, A4, A4p) were also identified in nine states and Puerto Rico, with higher frequencies in southern states like LA, FL and TX. This data suggests the need to evaluate if a restricted mtDNA haplotype diversity in the US honey bee populations could have negative impacts on the beekeeping sustainability of this country.
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Affiliation(s)
- Mohamed Alburaki
- USDA-ARS Bee Research Laboratory, Beltsville, MD, United States,*Correspondence: Mohamed Alburaki,
| | - Shayne Madella
- USDA-ARS Bee Research Laboratory, Beltsville, MD, United States
| | - Jillian Lopez
- USDA-ARS Bee Research Laboratory, Beltsville, MD, United States
| | - Maria Bouga
- Agricultural University of Athens, Athens, Greece
| | - Yanping Chen
- USDA-ARS Bee Research Laboratory, Beltsville, MD, United States
| | - Dennis vanEngelsdorp
- Department of Entomology, University of Maryland, College Park, MD, United States
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216
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First Evidence of Fowl Adenovirus Induced Inclusion Body Hepatitis in Chicken in Bangladesh. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:7253433. [PMID: 36636334 PMCID: PMC9831704 DOI: 10.1155/2023/7253433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/28/2022] [Accepted: 12/20/2022] [Indexed: 01/04/2023]
Abstract
Background The livestock sector contributes 1.90% to the GDP in Bangladesh during 2021-22. Poultry is one of the important subsectors struggling with diseases. Fowl adenoviruses (FAdVs) cause numerous diseases resulting in economic losses to the poultry industry worldwide. Several FAdV serotypes cause inclusion body hepatitis in chicken. Although FAdV infection was suspected, there was no confirmatory report from Bangladesh. The study was conducted to investigate the FAdV infection and antibodies in chicken. Methods A total of 50 samples, each composed of liver and spleen, were collected from different chickens of Gazipur, Dinajpur, and Panchagarh district. Each location belongs to A, B, and C poultry zones of Bangladesh, respectively. Viruses were detected by real-time PCR and conventional PCR. Blood samples (n = 303) were collected at the beginning and after the recovery from infection and tested by indirect ELISA. Sequencing of PCR products was done for serotyping and phylogenetic analysis. Results Clinical signs were observed including anorexia, drowsiness, ruffled feathers, reduced body weight, lack of uniformity, and high mortality (15-25%). Enlarged friable liver with yellow to tan color mottled with the focal soft area, fluid in pericardial sac, swollen and hemorrhagic kidneys, enlarged congested spleen and pancreas, etc. were found on postmortem examination. FAdVs were detected in 90% of the flocks except commercial layer flock from Dinajpur. Three serotypes, namely, 8b (70%), 11 (10%), and 5 (10%) were detected. Anti-FAdV antibody was detected in 80% flocks at the beginning of infection and in 90% of the flocks after recovery from infection. The antibody titer increases significantly (p < 0.05) after recovery from infection. Phylogenetic analysis revealed that the Bangladeshi FAdVs have close identity with viruses from Asia, Europe, and South and North America. Conclusions These findings suggested that several introductions of FAdVs were taken place in Bangladesh. To combat the disease, vaccination along with maintenance of biosecurity is essential.
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217
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Clonostachys rosea Strain ST1140: An Endophytic Plant-Growth-Promoting Fungus, and Its Potential Use in Seedbeds with Wheat-Grain Substrate. Curr Microbiol 2023; 80:36. [DOI: 10.1007/s00284-022-03146-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
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218
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Babarinde IA, Adeola AC, Djagoun CAMS, Nneji LM, Okeyoyin AO, Niba G, Wanzie NK, Oladipo OC, Adebambo AO, Bello SF, Ng'ang'a SI, Olaniyi WA, Okoro VMO, Adedeji BE, Olatunde O, Ayoola AO, Matouke MM, Wang YY, Sanke OJ, Oseni SO, Nwani CD, Murphy RW. Population structure and evolutionary history of the greater cane rat ( Thryonomys swinderianus) from the Guinean Forests of West Africa. Front Genet 2023; 14:1041103. [PMID: 36923796 PMCID: PMC10010571 DOI: 10.3389/fgene.2023.1041103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023] Open
Abstract
Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (FST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6-10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.
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Affiliation(s)
- Isaac A Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Chabi A M S Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Agboola O Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | - George Niba
- National Centre for Animal Husbandry and Veterinary Training, Jakiri, North West Region, Cameroon
| | - Ndifor K Wanzie
- Department of Zoology, University of Douala, Douala, Cameroon.,Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | - Ayotunde O Adebambo
- Animal Genetics & Biotechnology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Semiu F Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Said I Ng'ang'a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wasiu A Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Victor M O Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | | | - Omotoso Olatunde
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Adeola O Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China
| | - Moise M Matouke
- Department of Fisheries and Aquatic Resources Management, University of Buea, Buea, Cameroon
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Saidu O Oseni
- Department of Animal Sciences, Faculty of Agriculture, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Christopher D Nwani
- Department of Zoology and Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
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219
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Erol U, Sahin OF, Altay K. Molecular prevalence of bovine hemoplasmosis in Turkey with first detection of Mycoplasma wenyonii and Candidatus Mycoplasma haemobos in cattle and water buffalo. Vet Res Commun 2023; 47:207-215. [PMID: 35624402 DOI: 10.1007/s11259-022-09943-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/19/2022] [Indexed: 01/27/2023]
Abstract
Hemoplasma species can cause infection varying from mild to severe in a wide range of hosts, including cattle and water buffalo. Two hemoplasma species, Mycoplasma wenyonii and Candidatus Mycoplasma haemobos, have been reported in cattle and water buffalo from different parts of the world to date. There was a lack of information on the presence and distribution of these pathogens in Turkey despite the negative economic impact on livestock production. This study aimed to develop a duplex PCR assay amplifying the 16S rRNA gene, in order to analyze DNA samples obtained from 297 cattle and 360 water buffaloes, and to determine the molecular prevalence of bovine hemoplasma species in Sivas province. Bovine hemoplasma species were found in 94 of 297 (31.64%) cattle and in 17 of 360 (4.72%) water buffaloes in this study. Randomly selected six positives PCR products (three samples each species) obtained from cattle and water buffaloes were sequenced, and the consensus sequences were uploaded to GenBank. Nucleotide similarity of 96.97-100% was determined between M. wenyonii isolates obtained in this study and those of M. wenyonii isolates present in the GenBank database, whereas C. Mycoplasma haemobos isolates from this study shared 99.04-100% homology with the C. Mycoplasma haemobos isolates uploaded to the GenBank. With the current study, the molecular presence of M. wenyonii and C. Mycoplasma haemobos were documented for the first time in cattle and water buffaloes in Turkey. Considering the rate of prevalence, veterinarians should take precautions against bovine hemoplasma species to protect animal health.
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Affiliation(s)
- Ufuk Erol
- Department of Parasitology, Faculty of Veterinary Medicine, University of Sivas Cumhuriyet, 58140, Sivas, Turkey.
| | - Omer Faruk Sahin
- Department of Parasitology, Faculty of Veterinary Medicine, University of Sivas Cumhuriyet, 58140, Sivas, Turkey
| | - Kursat Altay
- Department of Parasitology, Faculty of Veterinary Medicine, University of Sivas Cumhuriyet, 58140, Sivas, Turkey
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Palasciano M, Zuluaga DL, Cerbino D, Blanco E, Aufiero G, D’Agostino N, Sonnante G. Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers. PLANTS (BASEL, SWITZERLAND) 2022; 12:136. [PMID: 36616264 PMCID: PMC9824393 DOI: 10.3390/plants12010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the 'Germersdorfer-Ferrovia' cluster, (iii) the 'Burlat' group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties.
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Affiliation(s)
- Marino Palasciano
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Diana L. Zuluaga
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Domenico Cerbino
- Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura (ALSIA) Pollino, C.da Piano Incoronata, 85048 Rotonda, Italy
| | - Emanuela Blanco
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Gaetano Aufiero
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
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Meza C, Valenzuela F, Echeverría-Vega A, Gomez A, Sarkar S, Cabeza RA, Arencibia AD, Quiroz K, Carrasco B, Banerjee A. Plant-growth-promoting bacteria from rhizosphere of Chilean common bean ecotype ( Phaseolus vulgaris L.) supporting seed germination and growth against salinity stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1052263. [PMID: 36618623 PMCID: PMC9814130 DOI: 10.3389/fpls.2022.1052263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Salinity abiotic stress is increasing day by day due to continuous global warming and climate change. This is also becoming one of the major causes behind the reduction in crop production. Plant-bacteria interaction plays an essential role in improving crop yield without using any chemical fertilizers. The present study aims to characterize the interaction between plant-growth-promoting bacteria (PGPB) and their role in mitigating salinity stress for local variety crops. Therefore, in this work, two PGPB, namely, Bacillus proteolyticus Cyn1 and Bacillus safensis Cyn2, were isolated from rhizospheric soil of the Chilean common bean ecotype "Sapito" (Phaseolus vulgaris L.), and their PGPB traits were analyzed. Cyn1 can produce NH3 and HCN and also secrete siderophores, whereas Cyn2 produced NH3 and siderophores but responded negatively to HCN production. Both the isolated bacteria have shown a positive result for ACC deaminase production, phosphate solubilization, and catalase enzyme secretion. Under all three tested abiotic stresses, i.e., temperature, water, and salinity, both the bacteria and their consortium have demonstrated positive responses. Cyn1 under temperature stress and water stress can produce a biofilm network to combat the stress. While under salinity stress, both the PGPB isolates indicated the production of stress components and cytoplasmic inclusion bodies. Based on the response, among all other abiotic stresses, salinity stress was chosen for further plant-bacteria interaction study and growth. Visible root colonization of the bacteria has been observed in comparison to the control. The germination index was 100% for all experimental setups of seed bacterization, both under control conditions and salinity stress. Both bacteria responded with good PGP traits that helped in the growth of healthy plants after the bacterial treatment in final pot experiments. Additionally, the consortium and the plants treated with Cyn1 have demonstrated high production of photosynthetic pigments in both experimental setups. Both B. proteolyticus Cyn1 and B. safensis Cyn2 have shown promising PGP characters and efficient response against toxicity related to salinity. Hence, both of these bacteria and consortium can be used for improved agricultural production of Chilean native common beans in the near future.
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Affiliation(s)
- Cynthia Meza
- Doctorado en Biotecnología Traslacional (DBT), Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
- Centro de Biotecnología de los Recursos Naturales (CENBio), Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
- Centro de Estudios en Alimentos Procesados (CEAP), Talca, Chile
| | | | - Alex Echeverría-Vega
- Centro de Investigación de Estudios Avanzados del Maule, Vicerrectoría de Investigación y Posgrado, Universidad Católica del Maule, Talca, Chile
| | - Aleydis Gomez
- Centro de Biotecnología de los Recursos Naturales (CENBio), Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
| | - Shrabana Sarkar
- Centro de Investigación de Estudios Avanzados del Maule, Vicerrectoría de Investigación y Posgrado, Universidad Católica del Maule, Talca, Chile
| | - Ricardo A. Cabeza
- Plant Nutrition Laboratory, Department of Crop Sciences, Faculty of Agricultural Sciences, University of Talca, Talca, Chile
| | - Ariel D. Arencibia
- Centro de Biotecnología de los Recursos Naturales (CENBio), Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
| | - Karla Quiroz
- Centro de Biotecnología de los Recursos Naturales (CENBio), Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
| | | | - Aparna Banerjee
- Centro de Biotecnología de los Recursos Naturales (CENBio), Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
- Centro de Investigación de Estudios Avanzados del Maule, Vicerrectoría de Investigación y Posgrado, Universidad Católica del Maule, Talca, Chile
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Mushtaq HMS, Kamran M, Saleh AA, Alatawi FJ. Evidence for Reconsidering the Taxonomic Status of Closely Related Oligonychus Species in punicae Complex (Acari: Prostigmata: Tetranychidae). INSECTS 2022; 14:3. [PMID: 36661932 PMCID: PMC9864387 DOI: 10.3390/insects14010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
To elucidate the taxonomic problems in species delineation within the Oligonychus punicae complex (O. punicae, O. mangiferus, and O. vitis) (Acari: Prostigmata: Tetranychidae), we performed morphological and molecular investigations on mite samples, collected from different hosts/countries. Thirty-nine samples of punicae complex, collected from Egypt, Pakistan, and Saudi Arabia (SA), did not show any considerable morphological differences in females and males. All 39 samples of the punicae complex resembled the original description of O. punicae, while the claimed Mexican O. punicae was distinctively different based on male aedeagus. Molecularly, the low nucleotide diversity ranged from 0% to 2.1% (ITS2-rDNA) and 0% to 1% (COI-mtDNA), and was observed among various DNA sequences of the punicae complex from Egypt, India, Israel, Pakistan, and SA, confirming their identity as one species. The high genetic divergence ranged from 17.2% to 18.8% (ITS2) and 9.2% to 10.2% (COI), observed between the claimed Mexican O. punicae and all other sequences of the punicae complex, indicating that the Mexican sample do not belong to O. punicae. Basing our findings on both morphological and molecular data, we can conclude that O. mangiferus and O. vitis are synonymized with O. punicae. Additionally, this study reveals that the claimed Mexican O. punicae needs to be re-identified.
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Affiliation(s)
- Hafiz Muhammad Saqib Mushtaq
- Acarology Research Laboratory, Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, P.O. Box No. 2460, Riyadh 11451, Saudi Arabia
| | - Muhammad Kamran
- Acarology Research Laboratory, Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, P.O. Box No. 2460, Riyadh 11451, Saudi Arabia
| | - Amgad A. Saleh
- Plant Pathology Laboratory, Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, P.O. Box No. 2460, Riyadh 11451, Saudi Arabia
| | - Fahad Jaber Alatawi
- Acarology Research Laboratory, Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, P.O. Box No. 2460, Riyadh 11451, Saudi Arabia
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Martínez-García L, González-Alba JM, Puerta T, Comunión A, Rodríguez-Jiménez MC, Orviz E, Sánchez-Conde M, Rodríguez-Domínguez M, Cantón R, Galán JC. Specific high-resolution scheme to improve understanding of the spatio-temporal dispersion of lymphogranuloma venereum epidemic. Front Microbiol 2022; 13:1056216. [PMID: 36605505 PMCID: PMC9808035 DOI: 10.3389/fmicb.2022.1056216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Lymphogranuloma venereum (LGV) is already endemic in vulnerable populations in several European countries; however, molecular epidemiology data with improved accuracy are necessary to better understand LGV epidemic in these countries. Current strategies to study the molecular epidemiology of LGV cases involve schemes based on a few genetic fragments of Chlamydia trachomatis, which have demonstrated limited discriminatory power for LGV. Therefore, this study aimed to propose a new combination of molecular markers based on the most variable genes of L-genotype genomes to improve the characterization of the current LGV epidemic in Madrid, Spain. Methods Four genes were selected according to their diversity index (CTLon_0054, CTLon_0087, CTLon_0243 and CTLon_0301) for use in combination with ompA. In silico and experimental studies were performed to compare the previously described multilocus sequence typing (MLST) schemes with our proposal. Moreover, the proposed scheme was applied (n = 68) to analyze the spatio-temporal spread of the LGV cases. Results Our proposal demonstrated higher diversity allowing the identification of three main groups compared to the previously published MLST based on hypervariable genes wherein only a single sequence type was identified. The temporal analysis showed that the major cluster was progressively diversifying, revealing a very active transmission chain. Furthermore, an L2b genome identical to that of the origin of the epidemic was detected, suggesting reintroductions or a low screening rate in vulnerable populations. The spatial distribution suggests that the selection and spread of new variants occurs from the central district to the peripheral regions. Discussion The scheme proposed in this study has proven to be useful for appropriate discrimination of LGV strains. This study, to our knowledge for the first time, demonstrates a spatio-temporal spread that increases our understanding and identifies areas with special susceptibility for maintenance of the endemic situation of LGV.
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Affiliation(s)
- Laura Martínez-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - José María González-Alba
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Teresa Puerta
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | | | - María Concepción Rodríguez-Jiménez
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Eva Orviz
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Matilde Sánchez-Conde
- Servicio de Enfermedades Infecciosas. Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Mario Rodríguez-Domínguez
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain,*Correspondence: Juan Carlos Galán,
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Population Genetics and Anastomosis Group's Geographical Distribution of Rhizoctonia solani Associated with Soybean. Genes (Basel) 2022; 13:genes13122417. [PMID: 36553683 PMCID: PMC9777564 DOI: 10.3390/genes13122417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Rhizoctonia solani is a species complex composed of many genetically diverse anastomosis groups (AG) and their subgroups. It causes economically important diseases of soybean worldwide. However, the global genetic diversity and distribution of R. solani AG associated with soybean are unknown to date. In this study, the global genetic diversity and distribution of AG associated with soybean were investigated based on rDNA-ITS sequences deposited in GenBank and published literature. The most prevalent AG, was AG-1 (40%), followed by AG-2 (19.13%), AG-4 (11.30%), AG-7 (10.43%), AG-11 (8.70%), AG-3 (5.22%) and AG-5 (3.48%). Most of the AG were reported from the USA and Brazil. Sequence analysis of internal transcribed spacers of ribosomal DNA separated AG associated with soybean into two distinct clades. Clade I corresponded to distinct subclades containing AG-2, AG-3, AG-5, AG-7 and AG-11. Clade II corresponded to subclades of AG-1 subgroups. Furthermore, AG and/or AG subgroups were in close proximity without corresponding to their geographical origin. Moreover, AG or AG subgroups within clade or subclades shared higher percentages of sequence similarities. The principal coordinate analysis also supported the phylogenetic and genetic diversity analyses. In conclusion, AG-1, AG-2, and AG-4 were the most prevalent AG in soybean. The clade or subclades corresponded to AG or AG subgroups and did not correspond to the AG's geographical origin. The information on global genetic diversity and distribution will be helpful if novel management measures are to be developed against soybean diseases caused by R. solani.
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Occurrence and Phylogenetic Description of Cystic Echinococcosis Isolate from Egyptian Camel ( Camelus Dromedarius). Helminthologia 2022; 59:253-264. [PMID: 36694828 PMCID: PMC9831517 DOI: 10.2478/helm-2022-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/17/2022] [Indexed: 12/23/2022] Open
Abstract
Cystic echinococcosis is one of the most significant cyclo-zoonotic diseases of major economic and public health significance worldwide. The current study was carried out to determine the epidemiological profile of cystic echinococcosis as well as to investigate its molecular and phylogenic status from one-humped camel (Camelus dromedarius) in the southern region of Egypt. In the present work, 110 camels freshly slaughtered at Daraw abattoirs, Aswan governorate were inspected for the presence of Hydatid cysts (HCs) visually and manually by palpation and incision, over a period of one year (June, 2018 - May, 2019). Furthermore, fourteen fertile hydatid cyst samples were collected from lungs of slaughtered camels. DNA extraction from two fertile samples was successfully achieved followed by phylogenetic analysis on two mitochondrial genes (cox1and nad1). Out of 110 camels slaughtered 11 (10 %) were found harboring hydatid cysts. The infection was found to prevail throughout the year, with the highest peak encountered in winter (45.5 %). The lungs were the most frequently infected organs (72.7 %) with liver cysts occurring at a significantly lower rate (27.3 %). The mean value of total protein, glucose, urea, cholesterol, magnesium, potassium, copper and creatinine was higher in cystic fluid from camels as compared to cattle. Blast and phylogenetic analysis on sequenced genes showed the presence of Echinococcus intermedius, originally the pig genotype (G7) in camels for the first time in Egypt. To the best of our knowledge, the current research provides a description of the current epidemiological and molecular situation of camel hydatidosis in the southern region of Egypt. Furthermore, the current results may have significant implications for hydatid disease control in the studied region.
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Mghazli N, Bruneel O, Zouagui R, Hakkou R, Sbabou L. Characterization of plant growth promoting activities of indigenous bacteria of phosphate mine wastes, a first step toward revegetation. Front Microbiol 2022; 13:1026991. [PMID: 36590425 PMCID: PMC9798287 DOI: 10.3389/fmicb.2022.1026991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Morocco holds the vast majority of the world's phosphate reserves, but due to the processes involved in extracting and commercializing these reserves, large quantities of de-structured, nutritionally deficient mine phosphate wastes are produced each year. In a semi-arid climate, these wastes severely hamper plant growth and development leading to huge unvegetated areas. Soil indigenous Plant Growth-Promoting Bacteria (PGPB) play a pivotal role in restauration of these phosphate mining wastes by revegetation, by increasing plants development, soil functioning, and nutrient cycling. The development of a vegetative cover above the degraded phosphate wastes, could stabilize and reintegrate these wastes in the surrounding environment. The current study's objectives were to isolate, characterize, and identify indigenous bacterial strains, and test their PGP activity in vitro and, for the best-performing strains in planta, in order to assess their potential for acting as biofertilizers. A quantitative test for the synthesis of auxin and the production of siderophores as well as a qualitative test for the solubilization of phosphate were performed on all isolated bacterial strains. The production of hydrogen cyanide (HCN), exopolysaccharides (EPS), and enzymes were also examined. Three bacteria, selected among the best PGPB of this study, were tested in planta to determine whether such indigenous bacteria could aid plant growth in this de-structured and nutrient-poor mining soil. Using 16S rRNA gene sequencing, 41 bacterial strains were isolated and 11 genera were identified: Acinetobacter, Agrococcus, Bacillus, Brevibacterium, Microbacterium, Neobacillus, Paenibacillus, Peribacillus, Pseudarthrobacter, Stenotrophomonas, and Raoultella. Among the three best performing bacteria (related to Bacillus paramycoides, Brevibacterium anseongense, and Stenotrophomonas rhizophila), only Stenotrophomonas rhizophila and Brevibacterium anseongense were able to significantly enhance Lupinus albus L. growth. The best inoculation results were obtained using the strain related to Stenotrophomonas rhizophila, improving the plant's root dry weight and chlorophyll content. This is also, to our knowledge, the first study to show a PGP activity of Brevibacterium anseongense.
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Affiliation(s)
- Najoua Mghazli
- Center of Research Plants and Microbial Biotechnologies, Biodiversity and Environment, Team of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco,HSM, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Odile Bruneel
- HSM, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Rahma Zouagui
- Center of Research Plants and Microbial Biotechnologies, Biodiversity and Environment, Team of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Rachid Hakkou
- Laboratoire des Matériaux Innovants, Energie et Développement Durable (IMED)_Laboratory, Faculty of Science and Technology, Cadi Ayyad University, Marrakesh, Morocco,Geology & Sustainable Mining Institute (GSMI), Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Laila Sbabou
- Center of Research Plants and Microbial Biotechnologies, Biodiversity and Environment, Team of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco,*Correspondence: Laila Sbabou,
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Altay K, Sahin OF, Erol U, Aytmirzakizi A. First molecular detection and phylogenetic analysis of Mycoplasma wenyonii and Candidatus Mycoplasma haemobos in cattle in different parts of Kyrgyzstan. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01292-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Matar N, Macadré C, Ammar GAG, Peres A, Collet B, Boustany NE, Rajjou L, As-Sadi F, Dufresne M, Ratet P. Identification of beneficial Lebanese Trichoderma spp. wheat endophytes. FRONTIERS IN PLANT SCIENCE 2022; 13:1017890. [PMID: 36531385 PMCID: PMC9755858 DOI: 10.3389/fpls.2022.1017890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Wheat is one of the most important crops in the world. Its production can be influenced by a diversity of beneficial and pathogenic rhizospheric microbes, including fungi. Amongst them, beneficial Trichoderma spp. can be used as alternatives to chemical fertilizers, as they are cheap and harmless to the environment. Our study aimed to isolate, identify, and characterize Trichoderma spp. from Lebanon associated with wheat. Two Trichoderma strains belonging to T. afroharzianum, and T. guizhouense species, were isolated and found to be endophytes, enhancing root growth and producing Indole-3-acetic acid. Inoculation also improved seedling development, and increased plant growth and yield. Furthermore, the two strains inhibit Fusarium growth in vitro. These Trichoderma spp. have thus the capacity to be used as organic fertilizers for wheat.
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Affiliation(s)
- Naeif Matar
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Department of Life & Earth Sciences, Faculty of Sciences I, Laboratory of Microbiology, Lebanese University, Beirut, Lebanon
| | - Catherine Macadré
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Gamal A. G. Ammar
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Biotechnology Unit, Plant Production Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Alexis Peres
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Boris Collet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Naim El Boustany
- Department of Biology, Faculty of Sciences I, Lebanese University, Beirut, Lebanon
| | - Loïc Rajjou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Falah As-Sadi
- Department of Life & Earth Sciences, Faculty of Sciences I, Laboratory of Microbiology, Lebanese University, Beirut, Lebanon
- The Lebanese University, Faculty of Agronomy, Beirut, Lebanon
| | - Marie Dufresne
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Pascal Ratet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
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Sakdapetsiri C, Ngaemthao W, Suriyachadkun C, Pinyakong O. Paeniglutamicibacter quisquiliarum sp. nov., isolated from midden soil waste. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748475 DOI: 10.1099/ijsem.0.005651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A Gram-stain-positive, irregular short-rod and non-motile bacterium, designated strain ABSL32-1T, was isolated from a soil sample collected from the Suphan Buri municipal solid waste disposal area. According to the results of a polyphasic taxonomic study, a novel species belonging to the genus Paeniglutamicibacter was described. Strain ABSL32-1T grew optimally at 20-25 °C and at pH 6.0-8.0 in the presence of 1 % (w/v) NaCl. The whole-cell sugars were ribose, mannose and glucose. The peptidoglycan structure contained A4α peptidoglycan (Lys-Glu; A11.54). The polar lipids contained digalactosyldiacylglycerol, diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids and two unidentified lipids. The major menaquinones were MK-9 and MK-10. The major cellular fatty acid was anteiso-C15 : 0 (70.1 %). Based on 16S rRNA gene sequence analysis, strain ABSL32-1T showed the highest similarity to Paeniglutamicibacter sulfureus DSM 20167T (99.5 %), followed by Paeniglutamicibacter antarcticus SPC26T (99.0 %) and Paeniglutamicibacter psychrophenolicus AG31T (98.8 %). The genome of strain ABSL32-1T is 4.4 Mbp with a DNA G+C content of 66.0 mol%. The average nucleotide identity values between strain ABSL32-1T and the type strains P. sulfureus DSM20167T, P. antarcticus SPC26T and P. psychrophenolicus AG31T were 86.6, 74.7 and 83.6 %, respectively. On the basis of phenotypic, chemotaxonomic and genotypic properties, strain ABSL32-1T is proposed to represent a novel species to be named Paeniglutamicibacter quisquiliarum sp. nov. The type strain is ABSL32-1T (=TBRC 14976T=NBRC 115252T).
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Affiliation(s)
- Chatsuda Sakdapetsiri
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Department of Plant Pathology, Faculty of Agriculture at Kamphaengsaen, Kasetsart University Kamphaengsaen Campus, Nakhon Pathom 73140, Thailand
| | - Wipaporn Ngaemthao
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand
| | - Chanwit Suriyachadkun
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand
| | - Onruthai Pinyakong
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok 10330, Thailand
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Park DS, Choi J, Kim HJ, Kim JY, Kim MH, Lee JY, Moon JC, Park HB, Park K, Yun JH, Oh Y, Choe S, Na KJ, Yoon J. Two Cases of Mange Mite (Sarcoptes scabiei) Infestation in Long-Tailed Goral (Naemorhedus caudatus) in Republic of Korea. THE KOREAN JOURNAL OF PARASITOLOGY 2022; 60:423-427. [PMID: 36588420 PMCID: PMC9806499 DOI: 10.3347/kjp.2022.60.6.423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/27/2022] [Indexed: 12/29/2022]
Abstract
The long-tailed goral, Naemorhedus caudatus (Mammalia: Bovidae), is one of the endangered animals in the Republic of Korea (Korea). Sarcoptic mange mites infested in diverse species of mammals, including humans, but no case has been reported in long-tailed gorals. We report 2 cases of mange mite, Sarcoptes scabiei, infestation in long-tailed gorals. Mange mites were sampled in the skin legions of the 2 long-tailed gorals, which were rescued in 2 different regions, Uljin-gun, Gyeongsangbuk-do and Cheorwon-gun, Gangwon-do, Korea. Our results showed that the ectoparasite was the itch mite that burrowed into skin and caused scabies on the morphological inspection and placed within the phylogenetic relations of the species. The present study confirmed for the first time in Korea that mange mites are pathogenic scabies of long-tailed goral. Closer surveillance of this pathogenic ectoparasite in zoonotic and infectious ecosystems is warranted.
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Affiliation(s)
- Da Som Park
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea
| | - Jin Choi
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea
| | - Hee-Jong Kim
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea
| | - Jin-Yong Kim
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea
| | - Min-Han Kim
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea
| | - Jin-Young Lee
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea
| | - Jeong Chan Moon
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea
| | - Hee-Bok Park
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea
| | - KyungMin Park
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea
| | - Jun Hee Yun
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea
| | - Yeonsu Oh
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Kangwon National University, Chuncheon 24341,
Korea
| | - Seongjun Choe
- Department of Parasitology, School of Medicine, Chungbuk National University, Cheongju 28644,
Korea
| | - Ki-Jeong Na
- Veterinary Laboratory Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644,
Korea
| | - Jongmin Yoon
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531,
Korea,Corresponding author ()
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Berckx F, Bandong CM, Wibberg D, Kalinowski J, Willemse J, Brachmann A, Simbahan J, Pawlowski K. Streptomyces coriariae sp. nov., a novel streptomycete isolated from actinorhizal nodules of Coriaria intermedia. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748598 DOI: 10.1099/ijsem.0.005603] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
An actinobacterial strain, CMB-FB, was isolated from surface-sterilized root nodules of a Coriaria intermedia plant growing along Halsema Highway in the province of Benguet (Luzon, Philippines). The 16S rRNA gene sequence of CMB-FB showed high sequence similarity to those of the type strains of Streptomyces rishiriensis (99.4 %), Streptomyces humidus (99.1 %), Streptomyces cacaoi subsp. asoensis (99.0 %), and Streptomyces phaeofaciens (98.6 %). The major menaquinones of CMB-FB were composed of MK-9(H4), MK-9(H6) and MK-9(H8), and there was a minor contribution of MK-9(H10). The polar lipid profile consisted of phosphatidylethanolamine, unidentified aminolipids and phospholipids, a glycophospholipid and four unidentified lipids. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The results of physiological analysis indicated that CMB-FB was mesophilic. The results of phylogenetic, genome-genome distance calculation and average nucleotide identity analysis indicated that the isolated strain represents the type strain of a novel species. On the basis of these results, strain CMB-FB (=DSM 112754T=LMG 32457T) is proposed as the type strain of the novel species Streptomyces coriariae sp. nov.
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Affiliation(s)
- Fede Berckx
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Cyndi Mae Bandong
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden.,Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany.,Present address: ELIXIR-DE, Institute of Bio- and Geosciences IBG-5 - Computational Metagenomics, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology, Leiden University, 2300 RA Leiden, Netherlands
| | | | - Jessica Simbahan
- Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
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232
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Srionrod N, Nooroong P, Poolsawat N, Minsakorn S, Watthanadirek A, Junsiri W, Sangchuai S, Chawengkirttikul R, Anuracpreeda P. Molecular characterization and genetic diversity of Babesia bovis and Babesia bigemina of cattle in Thailand. Front Cell Infect Microbiol 2022; 12:1065963. [PMID: 36523637 PMCID: PMC9744959 DOI: 10.3389/fcimb.2022.1065963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
Babesia bovis and B. bigemina are the most common tick-borne parasites that cause bovine babesiosis which effects livestock production, leading to economic losses in tropical and subtropical areas of the world. The aims of this study were to determine the molecular detection, genetic diversity and antigenicity prediction of B. bovis based on spherical body protein 2 (sbp-2) gene and B. bigemina based on rhoptry-associated protein 1a (rap-1a) gene in cattle in Thailand. By PCR assay, the molecular detection of B. bovis and B. bigemina infection revealed levels of 2.58% (4/155) and 5.80% (9/155), respectively. The phylograms showed that B. bovis sbp-2 and B. bigemina rap-1a sequences displayed 5 and 3 clades with similarity ranging between 85.53 to 100% and 98.28 to 100%, respectively, when compared within Thailand strain. Diversity analysis of sbp-2 and rap-1a sequences showed 18 and 4 haplotypes, respectively. The entropy analysis illustrated 104 and 7 polymorphic sites of sbp-2 and rap-1a nucleic acid sequences, respectively, while those of sbp-2 and rap-1a amino acid sequences showed 46 and 4 high entropy peaks, respectively. Motifs analysis exhibited the distribution and conservation among sbp-2 and rap-1a sequences. The continuous and discontinuous B-cell epitopes have also been evaluated in this work. Therefore, our findings may be used to ameliorate the understanding inputs of molecular phylogeny, genetic diversity and antigenicity of B. bovis and B. bigemina Thailand stains.
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Affiliation(s)
- Nitipon Srionrod
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Pornpiroon Nooroong
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Napassorn Poolsawat
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Sutthida Minsakorn
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Amaya Watthanadirek
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Witchuta Junsiri
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Siriphan Sangchuai
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand,Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Panat Anuracpreeda
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand,*Correspondence: Panat Anuracpreeda, ;
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233
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Munusamy M, Ching KC, Yang LK, Crasta S, Gakuubi MM, Chee ZY, Wibowo M, Leong CY, Kanagasundaram Y, Ng SB. Chemical elicitation as an avenue for discovery of bioactive compounds from fungal endophytes. Front Chem 2022; 10:1024854. [PMID: 36505735 PMCID: PMC9727085 DOI: 10.3389/fchem.2022.1024854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022] Open
Abstract
The present study investigated the molecular phylogeny, antimicrobial and cytotoxic activities of fungal endophytes obtained from the A*STAR Natural Organism Library (NOL) and previously isolated from Sungei Buloh Wetland Reserve, Singapore. Phylogenetic analysis based on ITS2 gene suggests that these isolates belong to 46 morphotypes and are affiliated to 23 different taxa in 17 genera of the Ascomycota phylum. Colletotrichum was the most dominant fungal genus accounting for 37% of all the isolates, followed by Diaporthe (13%), Phyllosticta (10.9%) and Diplodia (8.7%). Chemical elicitation using 5-azacytidine, a DNA methyltransferase inhibitor and suberoylanilide hydroxamic acid, a histone deacetylase inhibitor resulted in an increase in the number of active strains. Bioassay-guided isolation and structural elucidation yielded pestahivin and two new analogues from Bartalinia sp. F9447. Pestahivin and its related analogues did not exhibit antibacterial activity against Staphylococcus aureus but displayed strong antifungal activities against Candida albicans and Aspergillus brasiliensis, with IC50 values ranging from 0.46 ± 0.06 to 144 ± 18 µM. Pestahivin and its two analogues furthermore exhibited cytotoxic activity against A549 and MIA PACA-2 cancer cell lines with IC50 values in the range of 0.65 ± 0.12 to 42 ± 5.2 µM. The finding from this study reinforces that chemical epigenetic induction is a promising approach for the discovery of bioactive fungal secondary metabolites encoded by cryptic gene clusters.
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Affiliation(s)
- Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sharon Crasta
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhao Yan Chee
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore,*Correspondence: Siew Bee Ng,
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234
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Krusong W, La China S, Pothimon R, Gullo M. Defining Paenibacillus azoreducens (P8) and Acetobacter pasteurianus (UMCC 2951) strains performances in producing acetic acid. Front Microbiol 2022; 13:991688. [DOI: 10.3389/fmicb.2022.991688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, spore-forming bacteria isolated from saccharified rice were selected for producing acetic acid. From the screening of 15 strains, P8 strain was chosen as a candidate. The strain was identified as Paenibacillus azoreducens by 16S rRNA analysis (99.85% similarity with P. azoreducens CM1T). Acetic acid is the main component of vinegar but also an industrial commodity produced by chemical synthesis. Sustainable routes for obtaining acetic acid are of great interest for decreasing the environmental impact generated by chemical syntheses. Biological acetic acid production is effective for vinegar production by acetic acid bacteria, but it cannot economically compete with the chemical synthesis for producing it as a pure commodity. Considering the need to improve the yield of pure acetic acid produced by microbial conversions, in this study, P8 strain was chosen for designing processes in different fermentation conditions. Tests were conducted in single and semi-continuous systems, using rice wine as substrate. Acetic acid produced by P8 strain was compared with that of Acetobacter pasteurianus (UMCC 2951), a strain known for producing acetic acid from rice wine. Even though the fermentation performances of P. azoreducens P8 were slightly lower than those of acetic acid bacteria usually used for vinegar production, results highlight its suitability for producing acetic acid. The final acetic acid produced by P. azoreducens P8 was 73 g/L, in a single stage fermentation, without losses. In nine cycles of semi-continuous regime the average of acetification rate was 0.814 (g/L/days). Two main attributes of P. azoreducens P8 are of relevance for producing acetic acid, namely the ability to grow at temperature higher (+ 37°C), than mesophilic acetic acid bacteria, and the absence of cytoplasmic assimilation of acetic acid. These features allow to design multiple strains cultures, in which P. azoreducens can acts as a helper strain. Based on our results, the new isolate P. azoreducens P8 can be propagated in fermenting broths for boosting acetic acid production, under the selected conditions, and used in combination with acetic acid bacteria to produce biological acetic acid, as a non-food grade commodity.
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235
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Bohra SC, Zonunsanga HT, Das M, Purkayastha J, Biakzuala L, Lalremsanga HT. Morphological and molecular phylogenetic data reveal another new species of bent-toed gecko ( Cyrtodactylus Gray: Squamata: Gekkonidae) from Mizoram, India. J NAT HIST 2022. [DOI: 10.1080/00222933.2022.2119178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sanath Chandra Bohra
- Help Earth, Guwahati, India
- Wildlife Sciences, Department of Zoology, Gauhati University, Guwahati, Assam, India
| | | | - Madhurima Das
- Help Earth, Guwahati, India
- Department of Zoology, Assam Don Bosco University, Sonapur, India
| | | | - Lal Biakzuala
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, India
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, India
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236
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Assessing Molecular Diversity in Native and Introduced Populations of Red Wood Ant Formica paralugubris. Animals (Basel) 2022; 12:ani12223165. [PMID: 36428391 PMCID: PMC9687034 DOI: 10.3390/ani12223165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
The Formica rufa group comprises several ant species which are collectively referred to as "red wood ants" and play key roles in boreal forest ecosystems, where they are ecologically dominant and greatly influence habitat dynamics. Owing to their intense predatory activity, some of these species are used as biocontrol agents against several forest insect pests and for this aim in Italy, nearly 6000 ant nests were introduced from their native areas in the Alps to several Appeninic sites during the last century. In this work, we assessed and compared the genetic variability and structure of native and introduced populations of F. paralugubris, thus evaluating the extent of genetic drift that may have occurred since the time of introduction, using amplified fragment length polymorphism (AFLP) markers. PCR amplification with a fam_EcoRI-TAC/MseI-ATG primers combination produced a total of 147 scorable bands, with 17 identified as outlier loci. The genetic variation was higher in the introduced population compared to the native ones that, on the other hand, showed a higher diversity between nests. AMOVA results clearly pointed out that the overall genetic structure was dominated by among-worker variation, considering all populations, the Alpine vs. Apennine groups and the comparison among native and related introduced populations (all ranging between 77.84% and 79.84%). Genetic analyses unveiled the existence of six main different groups that do not entirely mirror their geographic subdivision, pointing towards a wide admixture between populations, but, at the same time, rapid diversification of some Apennine populations. Future studies based on high-throughput genomic methods are needed to obtain a thorough understanding of the effects of environmental pressure on the genetic structure and mating system of these populations.
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237
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Mitochondrial DNA variation of the caracal (Caracal caracal) in Iran and range-wide phylogeographic comparisons. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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238
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Cotuțiu VD, Ionică AM, Lefkaditis M, Cazan CD, Hașaș AD, Mihalca AD. Thelazia lacrymalis in horses from Romania: epidemiology, morphology and phylogenetic analysis. Parasit Vectors 2022; 15:425. [DOI: 10.1186/s13071-022-05532-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background
Equine thelaziosis is a neglected vector-borne parasitic disease in modern veterinary medicine, lacking recent reports. It is transmitted by Musca autumnalis, and potentially other Muscidae species, by ingesting the lachrymal secretions of its equine host. The distribution of both Thelazia lacrymalis and its intermediate hosts remains largely unknown throughout Europe, with most studies dating back 20 years. The aim of this study was to assess the presence, prevalence and distribution of T. lacrymalis in horses from Romania.
Methods
The eyes of 273 horses, slaughtered at two abattoirs from the Northwestern and Western regions of Romania, were examined for the presence of T. lacrymalis between March and November 2021. Upon detection, the nematodes were collected and morphologically identified using the keys from literature. Following identification, one specimen from each animal was selected for molecular analysis while the rest underwent detailed morphometric measurements. Mapping and distribution, according to ecoregions, was done using the QGis 3.20 software, while sequences obtained were compared to those available in GenBank through BLAST analysis using the MEGA X software.
Results
Of the 273 animals sampled, 12 (4.39%) were positive for Thelazia spp. infection. Eighty-seven nematodes were recovered, all morphologically identified as T. lacrymalis. The intensity of infestation varied between one and 33 nematodes/animal while five animals presented a bilateral infestation and seven a unilateral one. The highest prevalence was encountered in Pannonian ecoregion (12.12%) while the lowest was in the Alpine ecoregion (0%). Seventy-five intact specimens underwent detailed morphometric analysis, of the 18–20 parameters, resulting in notable differences in striation lengths compared to the data available in other reports. BLAST analysis identified a 96.46–98.60% similarity to the only other COI gene sequence available for T. lacrymalis.
Conclusions
The current study represents the first report of T. lacrymalis in horses in Romania. The low prevalence rates are probably linked to the wide use of macrocyclic lactones.
Graphic Abstract
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239
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Martí-Carreras J, Carrasco M, Gómez-Ponce M, Noguera-Julián M, Fisa R, Riera C, Alcover MM, Roura X, Ferrer L, Francino O. Identification of Leishmania infantum Epidemiology, Drug Resistance and Pathogenicity Biomarkers with Nanopore Sequencing. Microorganisms 2022; 10:2256. [PMID: 36422326 PMCID: PMC9697816 DOI: 10.3390/microorganisms10112256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 12/31/2023] Open
Abstract
The emergence of drug-resistant strains of the parasite Leishmania infantum infecting dogs and humans represents an increasing threat. L. infantum genomes are complex and unstable with extensive structural variations, ranging from aneuploidies to multiple copy number variations (CNVs). These CNVs have recently been validated as biomarkers of Leishmania concerning virulence, tissue tropism, and drug resistance. As a proof-of-concept to develop a novel diagnosis platform (LeishGenApp), four L. infantum samples from humans and dogs were nanopore sequenced. Samples were epidemiologically typed within the Mediterranean L. infantum group, identifying members of the JCP5 and non-JCP5 subgroups, using the conserved region (CR) of the maxicircle kinetoplast. Aneuploidies were frequent and heterogenous between samples, yet only chromosome 31 tetrasomy was common between all the samples. A high frequency of aneuploidies was observed for samples with long passage history (MHOM/TN/80/IPT-1), whereas fewer were detected for samples maintained in vivo (MCRI/ES/2006/CATB033). Twenty-two genes were studied to generate a genetic pharmacoresistance profile against miltefosine, allopurinol, trivalent antimonials, amphotericin, and paromomycin. MHOM/TN/80/IPT-1 and MCRI/ES/2006/CATB033 displayed a genetic profile with potential resistance against miltefosine and allopurinol. Meanwhile, MHOM/ES/2016/CATB101 and LCAN/ES/2020/CATB102 were identified as potentially resistant against paromomycin. All four samples displayed a genetic profile for resistance against trivalent antimonials. Overall, this proof-of-concept revealed the potential of nanopore sequencing and LeishGenApp for the determination of epidemiological, drug resistance, and pathogenicity biomarkers in L. infantum.
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Affiliation(s)
- Joan Martí-Carreras
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Marina Carrasco
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Marcel Gómez-Ponce
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Marc Noguera-Julián
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Roser Fisa
- Laboratori de Parasitologia, Departament de Biologia Sanitat i Mediambient, Facultat de Farmàcia I Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
| | - Cristina Riera
- Laboratori de Parasitologia, Departament de Biologia Sanitat i Mediambient, Facultat de Farmàcia I Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
| | - Maria Magdalena Alcover
- Laboratori de Parasitologia, Departament de Biologia Sanitat i Mediambient, Facultat de Farmàcia I Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
| | - Xavier Roura
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
- Hospital Clínic Veterinari, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Lluís Ferrer
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
- Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Olga Francino
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
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240
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Zakalyukina YV, Pavlov NA, Lukianov DA, Marina VI, Belozerova OA, Tashlitsky VN, Guglya EB, Osterman IA, Biryukov MV. A New Albomycin-Producing Strain of Streptomyces globisporus subsp. globisporus May Provide Protection for Ants Messor structor. INSECTS 2022; 13:1042. [PMID: 36421945 PMCID: PMC9693239 DOI: 10.3390/insects13111042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
There are several well-studied examples of protective symbiosis between insect host and symbiotic actinobacteria, producing antimicrobial metabolites to inhibit host pathogens. These mutualistic relationships are best described for some wasps and leaf-cutting ants, while a huge variety of insect species still remain poorly explored. For the first time, we isolated actinobacteria from the harvester ant Messor structor and evaluated the isolates' potential as antimicrobial producers. All isolates could be divided into two morphotypes of single and mycelial cells. We found that the most common mycelial morphotype was observed among soldiers and least common among larvae in the studied laboratory colony. The representative of this morphotype was identified as Streptomyces globisporus subsp. globisporus 4-3 by a polyphasic approach. It was established using a E. coli JW5503 pDualRep2 system that crude broths of mycelial isolates inhibited protein synthesis in reporter strains, but it did not disrupt the in vitro synthesis of proteins in cell-free extracts. An active compound was extracted, purified and identified as albomycin δ2. The pronounced ability of albomycin to inhibit the growth of entomopathogens suggests that Streptomyces globisporus subsp. globisporus may be involved in defensive symbiosis with the Messor structor ant against infections.
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Affiliation(s)
- Yuliya V. Zakalyukina
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Department of Soil Science, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Nikolay A. Pavlov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Valeria I. Marina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russia
| | - Vadim N. Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Elena B. Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova st. 1, 117997 Moscow, Russia
| | - Ilya A. Osterman
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Mikhail V. Biryukov
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
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241
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Li L, Delgado‐Viscogliosi P, Gerphagnon M, Viscogliosi E, Christaki U, Sime‐Ngando T, Monchy S. Taxonomic and functional dynamics during chytrid epidemics in an aquatic ecosystem. Mol Ecol 2022; 31:5618-5634. [PMID: 36028992 PMCID: PMC9826485 DOI: 10.1111/mec.16675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023]
Abstract
Fungal parasitism is common in plankton communities and plays a crucial role in the ecosystem by balancing nutrient cycling in the food web. Previous studies of aquatic ecosystems revealed that zoosporic chytrid epidemics represent an important driving factor in phytoplankton seasonal successions. In this study, host-parasite dynamics in Lake Pavin (France) were investigated during the spring diatom bloom while following chytrid epidemics using next generation sequencing (NGS). Metabarcoding analyses were applied to study changes in the eukaryotic microbial community throughout diatom bloom-chytrid epidemics. Relative read abundances of metabarcoding data revealed potential "beneficiaries" and "victims" during the studied period. Subsequently, metatranscriptomic analyses on samples before and during the chytrid epidemic unveiled the active part of the community and functional/metabolic dynamics in association with the progress of chytrid infection. Diatom functions involving lipases, transporters, histones, vacuolar systems, the proteasome, proteases and DNA/RNA polymerases were more abundant during the diatom bloom. Chytrid functions related to a parasitic lifestyle including invasion, colonization and stress tolerance were up-regulated during the chytrid epidemic. In addition, functions related to the degradation/metabolism of proteins, lipids and chitin were in higher proportion in the community during the epidemic event. Results of NGS and bioinformatics analyses offered a panorama of dynamic biodiversity and biological functioning of the community.
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Affiliation(s)
- Luen‐Luen Li
- Université du Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOGLaboratoire d'Océanologie et de GéosciencesWimereuxFrance
| | - Pilar Delgado‐Viscogliosi
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de LilleU1019 – UMR 9017 – CIIL – Centre d'’Infection et d'’Immunité de LilleLilleFrance
| | - Mélanie Gerphagnon
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023Clermont Université, Blaise PascalAubièreFrance
| | - Eric Viscogliosi
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de LilleU1019 – UMR 9017 – CIIL – Centre d'’Infection et d'’Immunité de LilleLilleFrance
| | - Urania Christaki
- Université du Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOGLaboratoire d'Océanologie et de GéosciencesWimereuxFrance
| | - Télesphore Sime‐Ngando
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023Clermont Université, Blaise PascalAubièreFrance
| | - Sébastien Monchy
- Université du Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOGLaboratoire d'Océanologie et de GéosciencesWimereuxFrance
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242
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Wu Y, Yu B, Zhang Y, Wang L, Wang H, Song W, Xiang W, Zhao J, Wang X. Description of a new strain of Streptomonospora nanhaiensis and reclassification of Streptomonospora halotolerans as a later heterotypic synonym of Streptomonospora nanhaiensis. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748423 DOI: 10.1099/ijsem.0.005611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
A novel actinomycete, designated strain NEAU-YY374, was isolated from root of wheat and a polyphasic taxonomic study was carried out. 16S rRNA gene sequence analysis indicated that strain NEAU-YY374 was closely related to Streptomonospora halotolerans NEAU-Jh2-17T (99.3 %) and Streptomonospora nanhaiensis 12A09T (98.6%). Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-YY374 formed a stable clade with S. halotolerans NEAU-Jh2-17T and S. nanhaiensis 12A09T in trees generated with two algorithms. Key morphological and chemotaxonomic properties also confirmed the affiliation of strain NEAU-YY374 to the genus Streptomonospora. The differences of DNA G+C contents among these three strains were all less than 1 %, and the digital DNA-DNA hybridization and the average nucleotide identity values were higher than the circumscription thresholds of species and subspecies, clearly indicating that the three strains should belong to the same species. Therefore, we concluded that strain NEAU-YY374 is a new strain of S. nanhaiensis. Meanwhile, S. halotolerans should be reclassified as a later heterotypic synonym of S. nanhaiensis according to the priority of publication and validation of the name.
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Affiliation(s)
- Yan Wu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Bing Yu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Yuting Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Lan Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Han Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Wenshuai Song
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
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243
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Murakami S, Kitamura T, Matsugo H, Yamamoto T, Mineshita K, Sakuyama M, Sasaki R, Takenaka-Uema A, Horimoto T. Detection and genetic characterization of bat MERS-related coronaviruses in Japan. Transbound Emerg Dis 2022; 69:3388-3396. [PMID: 36057949 DOI: 10.1111/tbed.14695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/22/2022] [Accepted: 08/29/2022] [Indexed: 02/04/2023]
Abstract
Betacoronaviruses, containing sarbecoviruses such as severe acute respiratory syndrome coronaviruses (SARS-CoV) and merbecovirus such as Middle East respiratory syndrome coronavirus (MERS-CoV), caused three human outbreaks in the past 2 decades; in particular, SARS-CoV-2 has caused the coronavirus disease 2019 pandemic. Since the ancestor of betacoronaviruses originated from wild bats, unidentified bat betacoronaviruses are presumed to be transmitted to humans in the future. In this study, we detected novel bat merbecoviruses from Vespertilio sinensis and Eptesicus japonensis, belonging to the family Vespertilionidae, in Japan. We found that these merbecoviruses were phylogenetically most closely related to the those previously detected in China. Alignment of the predicted receptor-binding motif on the spike proteins indicated that the Japanese bat merbecoviruses did not possess the specific amino acid residues that could be responsible for binding of MERS-CoV to the human dipeptidyl peptidase-4 receptor, which is unlikely to infect humans. This study demonstrated that bat merbecoviruses are widely conserved in multiple bat species of Vespertilionidae in East Asia, emphasizing the need for extensive epidemiological and biological studies on bat betacoronaviruses to facilitate the risk assessment of their spillover potential to humans.
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Affiliation(s)
- Shin Murakami
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomoya Kitamura
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,African Swine Fever Unit, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tokyo, Japan
| | - Hiromichi Matsugo
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Ko Mineshita
- NPO Corporation Association of Bat Conservation, Iwate, Japan
| | - Muneki Sakuyama
- NPO Corporation Association of Bat Conservation, Iwate, Japan
| | - Reiko Sasaki
- NPO Corporation Association of Bat Conservation, Iwate, Japan
| | - Akiko Takenaka-Uema
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Taisuke Horimoto
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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244
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Chen YS, Wang LT, Lin ST, Lee YS, Chang YC, Wu HC, Liao CY, Chen WH, Deng JN, Wang YH. Fructobacillus apis sp. nov., isolated from the gut of honeybee ( Apis mellifera). Int J Syst Evol Microbiol 2022; 72. [PMID: 36748588 DOI: 10.1099/ijsem.0.005613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A Gram-positive, facultatively anaerobic, catalase-negative, fructose-dependent strain (W13T) was isolated from the gut of honeybee (Apis mellifera). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain W13T represents a distinct line of descent within the genus Fructobacillus, with the closest neighbours being Fructobacillus broussonetiae BCRC 81240T (98.9 % sequence similarity) and Fructobacillus durionis DSM 19113T (96.8 % sequence similarity). Comparative sequencing of the additional phylogenetic markers rpoC and recA confirmed the 16S rRNA gene tree topology. The complete genome of strain W13T consisted of 1 292 712 bp with a G+C content of 48.3 mol%. Pairwise comparisons of the average nucleotide identity values and digital DNA-DNA hybridization values between the genomes of W13T and its close phylogenetic neighbours, F. broussonetiae BCRC 81240T and F. durionis DSM 19113T, resulted in 76.2-84.1 % and 20.2-27.6 %, respectively. The main cellular fatty acids of strain W13T were C16 : 0, C18 : 1 ω9c and C18 : 1 ω7c. Thus, we propose a novel species within the genus Fructobacillus, with the name Fructobacillus apis sp. nov. and the type strain is W13T (= NBRC 115637T=BCRC 81365T).
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Affiliation(s)
- Yi-Sheng Chen
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City 333, Taiwan, ROC
| | - Li-Ting Wang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Shih-Ting Lin
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City 333, Taiwan, ROC
| | - Yu-Chung Chang
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City 333, Taiwan, ROC
| | - Hui-Chung Wu
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City 333, Taiwan, ROC
| | - Chia-Yu Liao
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City 333, Taiwan, ROC
| | - Wei-Hua Chen
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City 333, Taiwan, ROC
| | - Jin-Nan Deng
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City 333, Taiwan, ROC
| | - Yu-Hsuan Wang
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City 333, Taiwan, ROC
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245
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Modi A, Singh S, Patki J, Padmadas N. Screening and identification of azo dye decolorizers from mangrove rhizospheric soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:83496-83511. [PMID: 35768712 DOI: 10.1007/s11356-022-21610-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Removal of synthetic textile dyes poses a challenge to the textile industry and a threat to the environment's flora and fauna. These dyes are recalcitrant and not very amenable to physical and chemical techniques of degradation. Hence, several studies on alternative bioremediation methods involving plants, plant roots, single microbes, or a consortium of microbes for the decolorization of dyes have been carried out. In the present study, potent bacteria for dye decolorization were isolated from rhizospheric soil of mangrove plants collected from Kamothe, Navi Mumbai, India. Of the 20 isolates obtained after enrichment, seven isolates were used for further screening of efficient decolorization ability in minimal basal media containing 10% glucose, 2.5% trace metal solution, and 0.1% of Methyl Orange (MO) dye concentration. Physiological parameters to optimize the decolorization of dye at optimum pH, temperature, and incubation time were studied for all the seven isolates. UV-vis and Fourier transform infrared spectroscopy were used to investigate dye decolorization. The seven isolates were characterized morphologically, biochemically, and molecular identification of these bacterial isolates was performed by 16S rRNA sequence analysis. The isolates were identified as Bacillus paramycoides, Pseudomonas taiwanensis, Citrobacter murliniae, Acinetobacter pitti, Exiguobacterium acetylicum, Psychrobacter celer, and Aeromonas taiwanensis. Out of these, Aeromonas taiwanensis has shown exceptional capacity by ~ 100% decolorization of azo dye in minimum time.
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Affiliation(s)
- Akhilesh Modi
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382011, Gujarat, India
- School of Biotechnology and Bioinformatics, D.Y Patil Deemed to Be University, Navi Mumbai, 400706, India
| | - Sunita Singh
- School of Biotechnology and Bioinformatics, D.Y Patil Deemed to Be University, Navi Mumbai, 400706, India.
| | - Jyoti Patki
- School of Biotechnology and Bioinformatics, D.Y Patil Deemed to Be University, Navi Mumbai, 400706, India
| | - Naveen Padmadas
- School of Biotechnology and Bioinformatics, D.Y Patil Deemed to Be University, Navi Mumbai, 400706, India
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246
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Dreni L, Ferrándiz C. Tracing the Evolution of the SEPALLATA Subfamily across Angiosperms Associated with Neo- and Sub-Functionalization for Reproductive and Agronomically Relevant Traits. PLANTS (BASEL, SWITZERLAND) 2022; 11:2934. [PMID: 36365387 PMCID: PMC9656651 DOI: 10.3390/plants11212934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
SEPALLATA transcription factors (SEP TFs) have been extensively studied in angiosperms as pivotal components of virtually all the MADS-box tetrameric complex master regulators of floral organ identities. However, there are published reports that suggest that some SEP members also regulate earlier reproductive events, such as inflorescence meristem determinacy and inflorescence architecture, with potential for application in breeding programs in crops. The SEP subfamily underwent a quite complex pattern of duplications during the radiation of the angiosperms. Taking advantage of the many whole genomic sequences now available, we present a revised and expanded SEP phylogeny and link it to the known functions of previously characterized genes. This snapshot supports the evidence that the major SEP3 clade is highly specialized for the specification of the three innermost floral whorls, while its sister LOFSEP clade is functionally more versatile and has been recruited for diverse roles, such as the regulation of extra-floral bract formation and inflorescence determinacy and shape. This larger pool of angiosperm SEP genes confirms previous evidence that their evolution was driven by whole-genome duplications rather than small-scale duplication events. Our work may help to identify those SEP lineages that are the best candidates for the improvement of inflorescence traits, even in far distantly related crops.
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247
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Huang Y, Han Y, Li Z, Li X, Li Z, Liu P, Liu X, Cheng Q, Fan F, Kan B, Liang W. TssI2-TsiI2 of Vibrio fluvialis VflT6SS2 delivers pesticin domain-containing periplasmic toxin and cognate immunity that modulates bacterial competitiveness. Gut Microbes 2022; 14:2136460. [PMID: 36288406 PMCID: PMC9620997 DOI: 10.1080/19490976.2022.2136460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Vibrio fluvialis is a halophilic Gram-negative bacterium regarded as an emerging unusual enteric pathogen of increasing public health concern. Our previous work has identified two type VI secretion systems (T6SSs) in V. fluvialis, VflT6SS1, and VflT6SS2, and the latter is functional in mediating interbacterial competitiveness. However, its antibacterial effectors remain to be clarified. In this work, we focused on a new potential effector/immunity pair TssI2/TsiI2. Bioinformatics analysis revealed that the C-terminal domain of TssI2 belongs to a widespread family of pesticin, and its antibacterial toxicity and corresponding protection by TsiI2 were proved via bacterial killing assays, and their action sites were localized to the periplasm of bacterial cells. The interaction of TssI2 and TsiI2 was demonstrated by the bacterial adenylate cyclase two-hybrid, protein pull-down and isothermal titration calorimetry assays. Site-directed mutagenesis demonstrated that, in addition to Glu-844, Thr-863, and Asp-869, which correspond to three reported residues in pesticin of Yersinia pestis, additional residues including Phe-837, Gly-845, Tyr-851, Gly-867, Gln-963, Trp-975, and Arg-1000 were also proved to be crucial to the bactericidal activity of TssI2. Muramidase/lysozyme-related peptidoglycan (PG) hydrolase activities of TssI2 and its variants were validated with permeabilized Escherichia coli cells and purified PG substrate. Based on sequence homologies at C-terminals in various V. fluvialis isolates, TssI2 was subdivided into five clusters (12-22% identity among them), and the antibacterial activities of representative effectors from other four Clusters were also confirmed through periplasmic over-expression in E. coli host. Two selected cognate immunities were proved to confer protection against the toxicities of their effectors. Additionally, TsiI2, which belongs to Cluster I, exhibited cross-protection to effector from Cluster V. Together, current findings expand our knowledge of the diversity and consistency of evolved VgrG effectors in V. fluvialis and on how VflT6SS2 mediates a competitive advantage to gain a better survival.
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Affiliation(s)
- Yuanming Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaorui Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhe Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ping Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoshu Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qian Cheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fenxia Fan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,CONTACT Biao Kan
| | - Weili Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Weili Liang State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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248
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Akaishi T, Fujiwara K, Ishii T. Insertion/deletion hotspots in the Nsp2, Nsp3, S1, and ORF8 genes of SARS-related coronaviruses. BMC Ecol Evol 2022; 22:123. [PMID: 36307763 PMCID: PMC9616624 DOI: 10.1186/s12862-022-02078-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/11/2022] [Indexed: 11/20/2022] Open
Abstract
The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains many insertions/deletions (indels) from the genomes of other SARS-related coronaviruses. Some of the identified indels have recently reported to involve relatively long segments of 10-300 consecutive bases and with diverse RNA sequences around gaps between virus species, both of which are different characteristics from the classical shorter in-frame indels. These non-classical complex indels have been identified in non-structural protein 3 (Nsp3), the S1 domain of the spike (S), and open reading frame 8 (ORF8). To determine whether the occurrence of these non-classical indels in specific genomic regions is ubiquitous among broad species of SARS-related coronaviruses in different animal hosts, the present study compared SARS-related coronaviruses from humans (SARS-CoV and SARS-CoV-2), bats (RaTG13 and Rc-o319), and pangolins (GX-P4L), by performing multiple sequence alignment. As a result, indel hotspots with diverse RNA sequences of different lengths between the viruses were confirmed in the Nsp2 gene (approximately 2500-2600 base positions in the overall 29,900 bases), Nsp3 gene (approximately 3000-3300 and 3800-3900 base positions), N-terminal domain of the spike protein (21,500-22,500 base positions), and ORF8 gene (27,800-28,200 base positions). Abnormally high rate of point mutations and complex indels in these regions suggest that the occurrence of mutations in these hotspots may be selectively neutral or even benefit the survival of the viruses. The presence of such indel hotspots has not been reported in different human SARS-CoV-2 strains in the last 2 years, suggesting a lower rate of indels in human SARS-CoV-2. Future studies to elucidate the mechanisms enabling the frequent development of long and complex indels in specific genomic regions of SARS-related coronaviruses would offer deeper insights into the process of viral evolution.
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Affiliation(s)
- Tetsuya Akaishi
- grid.69566.3a0000 0001 2248 6943Department of Education and Support for Regional Medicine, Tohoku University, Seiryo-machi 1-1, Aoba-ku, 980-8574 Sendai, Miyagi Japan ,grid.69566.3a0000 0001 2248 6943COVID-19 Testing Center, Tohoku University, Sendai, Japan
| | - Kei Fujiwara
- grid.260433.00000 0001 0728 1069Department of Gastroenterology and Metabolism, Nagoya City University, Nagoya, Japan
| | - Tadashi Ishii
- grid.69566.3a0000 0001 2248 6943Department of Education and Support for Regional Medicine, Tohoku University, Seiryo-machi 1-1, Aoba-ku, 980-8574 Sendai, Miyagi Japan ,grid.69566.3a0000 0001 2248 6943COVID-19 Testing Center, Tohoku University, Sendai, Japan
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249
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Distinct HIV-1 Population Structure across Meningeal and Peripheral T Cells and Macrophage Lineage Cells. Microbiol Spectr 2022; 10:e0250822. [PMID: 36173332 PMCID: PMC9602438 DOI: 10.1128/spectrum.02508-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
HIV-1 sequence population structure among brain and nonbrain cellular compartments is incompletely understood. Here, we compared proviral pol and env high-quality consensus single-molecule real-time (SMRT) sequences derived from CD3+ T cells and CD14+ macrophage lineage cells from meningeal or peripheral (spleen, blood) tissues obtained at autopsy from two individuals with viral suppression on antiretroviral therapy (ART). Phylogenetic analyses showed strong evidence of population structure between CD3+ and CD14+ virus populations. Distinct env variable-region characteristics were also found between CD3+ and CD14+ viruses. Furthermore, shared macrophage-tropic amino acid residues (env) and drug resistance mutations (pol) between meningeal and peripheral virus populations were consistent with the meninges playing a role in viral gene flow across the blood-brain barrier. Overall, our results point toward potential functional differences among meningeal and peripheral CD3+ and CD14+ virus populations and a complex evolutionary history driven by distinct selection pressures and/or viral gene flow. IMPORTANCE Different cell types and/or tissues may serve as a reservoir for HIV-1 during ART-induced viral suppression. We compared proviral pol and env sequences from CD3+ T cells and CD14+ macrophage lineage cells from brain and nonbrain tissues from two virally suppressed individuals. We found strong evidence of viral population structure among cells/tissues, which may result from distinct selective pressures across cell types and anatomic sites.
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250
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Morozov A, Nirca V, Victorova A, Poppert S, Frickmann H, Yamada C, Kacena MA, Rata S, Movila A. SARS-CoV-2 from COVID-19 Patients in the Republic of Moldova: Whole-Genome Sequencing Results. Viruses 2022; 14:2310. [PMID: 36298865 PMCID: PMC9610950 DOI: 10.3390/v14102310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Since the onset of the COVID-19 pandemic, no viral genome sequences of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have been documented from the Republic of Moldova, a developing country geographically located in Eastern Europe between Romania and Ukraine. Here, we report the analysis of 96 SARS-CoV-2 sequences from Delta and Omicron variants of the SARS-CoV-2 cases in the Republic of Moldova obtained between August and November 2021 and between January and May 2022. Comparison to global viral sequences showed that among the Delta variant of the SARS-CoV-2, AY.122 (n = 25), followed by AY.4.2.3 (n = 6), AY.4 (n = 5), AY.43 (n = 3), AY.98.1 (n = 3), B.1.617.2 (n = 1), AY.125 (n = 1), AY.54 (n = 1), AY.9 (n = 1), AY.126 (n = 1), and AY.33 (n = 1) were the most frequently found lineages. Furthermore, 10 lineages of the Omicron variant, namely, BA.2 (n = 14), followed by BA.2.9 (n = 10), BA.1 (n = 5), BA.1.1 (n = 5), BA.1.18 (n = 4), BA.1.15.1 (n = 3), BA.1.17.2 (n = 2), BA.1.17 (n = 2), BA.1.15 (n = 1), and BA.2.1 (n = 1) were detected. In addition, we also identified the impact of the military crisis between Russia and Ukraine, when the COVID-19 epidemiological rules collapsed, on the distribution of Delta and Omicron variants in the Republic of Moldova. Additional studies are warranted to characterize further the impact of the war between Russia and Ukraine on the genomic epidemiology of the SARS-CoV-2 in the Republic of Moldova and Eastern Europe.
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Affiliation(s)
- Alexandr Morozov
- Molecular Biology Department, Imunotehnomed Ltd., MD-2001 Chisinau, Moldova
- Laboratory of Systematics and Molecular Phylogeny, Institute of Zoology, MD-2028 Chisinau, Moldova
| | - Vadim Nirca
- Molecular Biology Department, Imunotehnomed Ltd., MD-2001 Chisinau, Moldova
| | - Anna Victorova
- Molecular Biology Department, Imunotehnomed Ltd., MD-2001 Chisinau, Moldova
| | - Sven Poppert
- Diagnostic Department, Bernhard Nocht Institute for Tropical Medicine Hamburg, 20095 Hamburg, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20095 Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Chiaki Yamada
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN 46201, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46201, USA
| | - Melissa A. Kacena
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46201, USA
| | - Sergiu Rata
- Molecular Biology Department, Imunotehnomed Ltd., MD-2001 Chisinau, Moldova
| | - Alexandru Movila
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN 46201, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46201, USA
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