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Akahori M, Miyazaki A, Koinuma H, Tokuda R, Iwabuchi N, Kitazawa Y, Maejima K, Namba S, Yamaji Y. Use of the 23S rRNA gene as a target template in the universal loop-mediated isothermal amplification (LAMP) of genomic DNA from phytoplasmas. Microbiol Spectr 2024; 12:e0010624. [PMID: 38534170 PMCID: PMC11064480 DOI: 10.1128/spectrum.00106-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
Plant-pathogenic bacteria cause numerous diseases in host plants and can result in serious damage. Timely and accurate diagnostic techniques are, therefore, crucial. While advances in molecular techniques have led to diagnostic systems able to distinguish known plant pathogens at the species or strain level, systems covering larger categories are mostly lacking. In this study, a specific and universal LAMP-based diagnostic system was developed for phytoplasmas, a large group of insect-borne plant-pathogenic bacteria that cause significant agricultural losses worldwide. Targeting the 23S rRNA gene of phytoplasma, the newly designed primer set CaPU23S-4 detected 31 'Candidatus Phytoplasma' tested within 30 min. This primer set also showed high specificity, without false-positive results for other bacteria (including close relatives of phytoplasmas) or healthy plants. The detection sensitivity was ~10,000 times higher than that of PCR methods for phytoplasma detection. A simple, rapid method of DNA extraction, by boiling phytoplasma-infected tissues, was developed as well. When used together with the universal LAMP assay, it enabled the prompt and accurate detection of phytoplasmas from plants and insects. The results demonstrate the potential of the 23S rRNA gene as a versatile target for the LAMP-based universal detection of bacteria at the genus level and provide a novel avenue for exploring this gene as molecular marker for phytoplasma presence detection.IMPORTANCEPhytoplasmas are associated with economically important diseases in crops worldwide, including lethal yellowing of coconut palm, "flavescence dorée" and "bois noir" of grapevine, X-disease in stone fruits, and white leaf and grassy shoot in sugarcane. Numerous LAMP-based diagnostic assays, mostly targeting the 16S rRNA gene, have been reported for phytoplasmas. However, these assays can only detect a limited number of 'Candidatus Phytoplasma' species, whereas the genus includes at least 50 of these species. In this study, a universal, specific, and rapid diagnostic system was developed that can detect all provisionally classified phytoplasmas within 1 h by combining the LAMP technique targeting the 23S rRNA gene with a simple method for DNA extraction. This diagnostic system will facilitate the on-site detection of phytoplasmas and may aid in the discovery of new phytoplasma-associated diseases and putative insect vectors, irrespective of the availability of infrastructure and experimental resources.
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Affiliation(s)
- Mako Akahori
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Akio Miyazaki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroaki Koinuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryosuke Tokuda
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Bennypaul H, Sanderson D, Donaghy P, Abdullahi I. Development of a Real-Time PCR Assay for the Detection and Identification of Rubus Stunt Phytoplasma in Rubus spp. PLANT DISEASE 2023; 107:2296-2306. [PMID: 36611241 DOI: 10.1094/pdis-09-22-2193-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Rubus stunt, caused by 'Candidatus Phytoplasma rubi' (Rubus stunt phytoplasma; RSP), is an economically important disease of Rubus. This disease occurs in wild and cultivated Rubus spp. in Europe but has not been reported from North America; however, its major leafhopper vector is well established in western Canada and the U.S.A. RSP has the potential to impact the cane-fruit industry by significantly compromising yields and impacting export potential for Rubus propagation material. To mitigate the risk of this disease entering or establishing, import and export testing of propagation material is a phytosanitary requirement in Canada, the U.S.A., and other countries regulating RSP. In the absence of a specific test for RSP, the current testing scheme involves the use of a generic test to screen for phytoplasmas followed by additional time-consuming procedures to confirm the phytoplasma species. In this study, a real-time PCR assay, targeting a 154-bp region of tuf gene, was developed for sensitive and specific detection of RSP in Rubus spp. The developed assay detected a minimum of five target copies, and no cross-reactivity was observed even with the 'Ca. P. rubi'-related strain associated with blackberry witches' broom, which differs from RSP only by a single nucleotide polymorphism in the target region. Repeatability of the developed assay was checked on two real-time PCR platforms with acceptable results. In conclusion, this real-time PCR assay provides a sensitive and specific detection of RSP for mitigating the introduction and spread of Rubus stunt disease in Rubus spp.
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Affiliation(s)
- Harvinder Bennypaul
- Centre for Plant Health - Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, British Columbia V8L 1H3, Canada
| | - Daniel Sanderson
- Centre for Plant Health - Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, British Columbia V8L 1H3, Canada
| | - Peri Donaghy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Ismail Abdullahi
- Centre for Plant Health - Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, British Columbia V8L 1H3, Canada
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3
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Kirdat K, Tiwarekar B, Sathe S, Yadav A. From sequences to species: Charting the phytoplasma classification and taxonomy in the era of taxogenomics. Front Microbiol 2023; 14:1123783. [PMID: 36970684 PMCID: PMC10033645 DOI: 10.3389/fmicb.2023.1123783] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
Phytoplasma taxonomy has been a topic of discussion for the last two and half decades. Since the Japanese scientists discovered the phytoplasma bodies in 1967, the phytoplasma taxonomy was limited to disease symptomology for a long time. The advances in DNA-based markers and sequencing improved phytoplasma classification. In 2004, the International Research Programme on Comparative Mycoplasmology (IRPCM)- Phytoplasma/Spiroplasma Working Team – Phytoplasma taxonomy group provided the description of the provisional genus ‘Candidatus Phytoplasma’ with guidelines to describe the new provisional phytoplasma species. The unintentional consequences of these guidelines led to the description of many phytoplasma species where species characterization was restricted to a partial sequence of the 16S rRNA gene alone. Additionally, the lack of a complete set of housekeeping gene sequences or genome sequences, as well as the heterogeneity among closely related phytoplasmas limited the development of a comprehensive Multi-Locus Sequence Typing (MLST) system. To address these issues, researchers tried deducing the definition of phytoplasma species using phytoplasmas genome sequences and the average nucleotide identity (ANI). In another attempts, a new phytoplasma species were described based on the Overall Genome relatedness Values (OGRI) values fetched from the genome sequences. These studies align with the attempts to standardize the classification and nomenclature of ‘Candidatus’ bacteria. With a brief historical account of phytoplasma taxonomy and recent developments, this review highlights the current issues and provides recommendations for a comprehensive system for phytoplasma taxonomy until phytoplasma retains ‘Candidatus’ status.
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Affiliation(s)
- Kiran Kirdat
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University, Pune, India
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, India
| | - Bhavesh Tiwarekar
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University, Pune, India
| | - Shivaji Sathe
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, India
| | - Amit Yadav
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University, Pune, India
- *Correspondence: Amit Yadav, ,
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4
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Pusz-Bochenska K, Perez-Lopez E, Wist TJ, Bennypaul H, Sanderson D, Green M, Dumonceaux TJ. Multilocus sequence typing of diverse phytoplasmas using hybridization probe-based sequence capture provides high resolution strain differentiation. Front Microbiol 2022; 13:959562. [PMID: 36246242 PMCID: PMC9556853 DOI: 10.3389/fmicb.2022.959562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022] Open
Abstract
Phytoplasmas are insect-vectored, difficult-to-culture bacterial pathogens that infect a wide variety of crop and non-crop plants, and are associated with diseases that can lead to significant yield losses in agricultural production worldwide. Phytoplasmas are currently grouped in the provisional genus ‘Candidatus Phytoplasma’, which includes 49 ‘Candidatus’ species. Further differentiation of phytoplasmas into ribosomal groups is based on the restriction fragment length polymorphism (RFLP) pattern of the 16S rRNA-encoding operon, with more than 36 ribosomal groups (16Sr) and over 100 subgroups reported. Since disease symptoms on plants are not associated with phytoplasma identity, accurate diagnostics is of critical importance to manage disease associated with these microorganisms. Phytoplasmas are typically detected from plant and insect tissue using PCR-based methods targeting universal taxonomic markers. Although these methods are relatively sensitive, specific and are widely used, they have limitations, since they provide limited resolution of phytoplasma strains, thus necessitating further assessment of biological properties and delaying implementation of mitigation measures. Moreover, the design of PCR primers that can target multiple loci from phytoplasmas that differ at the sequence level can be a significant challenge. To overcome these limitations, a PCR-independent, multilocus sequence typing (MLST) assay to characterize an array of phytoplasmas was developed. Hybridization probe s targeting cpn60, tuf, secA, secY, and nusA genes, as well as 16S and rp operons, were designed and used to enrich DNA extracts from phytoplasma-infected samples for DNA fragments corresponding to these markers prior to Illumina sequencing. This method was tested using different phytoplasmas including ‘Ca. P. asteris’ (16SrI-B), ‘Ca. P. pruni’ (16SrIII-A),‘Ca. P. prunorum’ (16SrX-B), ‘Ca. P. pyri’ (16SrX-C), ‘Ca. P. mali’ (16SrX-A), and ‘Ca. P. solani’ (16SrXII-A). Thousands of reads were obtained for each gene with multiple overlapping fragments, which were assembled to generate full-length (typically >2 kb), high-quality sequences. Phytoplasma groups and subgroups were accurately determined based on 16S ribosomal RNA and cpn60 gene sequences. Hybridization-based MLST facilitates the enrichment of target genes of phytoplasmas and allows the simultaneous determination of sequences corresponding to seven different markers. In this proof-of-concept study, hybridization-based MLST was demonstrated to be an efficient way to generate data regarding ‘Ca. Phytoplasma’ species/strain differentiation.
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Affiliation(s)
- Karolina Pusz-Bochenska
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edel Perez-Lopez
- Centre de Recherche et D'innovation sur les Végétaux (CRIV), Faculté des Sciences de L'agriculture et de L'alimentation, Département de Phytologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Tyler J. Wist
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Harvinder Bennypaul
- Canadian Food Inspection Agency (CFIA), Sidney Laboratory, Centre for Plant Health, North Saanich, BC, Canada
| | - Daniel Sanderson
- Canadian Food Inspection Agency (CFIA), Sidney Laboratory, Centre for Plant Health, North Saanich, BC, Canada
| | - Margaret Green
- Canadian Food Inspection Agency (CFIA), Sidney Laboratory, Centre for Plant Health, North Saanich, BC, Canada
| | - Tim J. Dumonceaux
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Tim J. Dumonceaux,
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5
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Soto N, Helmick EE, Harrison NA, Bahder BW. Genetic Variability of Palm Lethal Decline Phytoplasmas in the Caribbean Basin and Florida, U.S.A., Based on a Multilocus Analysis. PHYTOPATHOLOGY 2021; 111:2203-2212. [PMID: 34844420 DOI: 10.1094/phyto-04-21-0130-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Palm lethal decline phytoplasmas are an important group of plant pathogens that cause death in a variety of palm species throughout the Caribbean basin and the southeastern United States. The 16SrIV-D phytoplasma was introduced to the state of Florida, United States; it has since caused severe economic losses to the green industries of Florida and is threating natural ecosystems because of its ability to infect the native palm Sabal palmetto. In this study, the genetic variability of the 16SrIV-D phytoplasma was assessed over a 10-year period to determine if multiple introductions had occurred or if natural mutations were occurring. Furthermore, the genetic variability of the palm lethal decline phytoplasma group (16SrIV) was assessed with a multiple locus analysis using the 16S ribosomal RNA gene, the 16S-23S intergenic spacer region, and secA and groEL genes. Overall, no variability of the 16SrIV-D phytoplasma was documented in Florida over a 10-year period. The multilocus analysis showed support for three distinct species of the phytoplasma in the Caribbean basin that infect palms and further support that the 16SrIV-C from Tanzania is not closely related. Furthermore, 16SrIV-B and 16SrIV-D were found to be the same phytoplasma based on 100% identity between the two based on intergenic spacer region, secA, and groEL analysis. This study represents the first robust, multilocus analysis of palm-infecting phytoplasmas from the Caribbean and sheds light on the phylogeny and evolution of the group.
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Affiliation(s)
- Noemi Soto
- Department of Entomology and Nematology, University of Florida Fort Lauderdale Research and Education Center, Davie, FL 33314-7719
| | - Ericka E Helmick
- Department of Entomology and Nematology, University of Florida Fort Lauderdale Research and Education Center, Davie, FL 33314-7719
| | - Nigel A Harrison
- Department of Plant Pathology, University of Florida Fort Lauderdale Research and Education Center, Davie, FL 33314-7719
| | - Brian W Bahder
- Department of Entomology and Nematology, University of Florida Fort Lauderdale Research and Education Center, Davie, FL 33314-7719
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6
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Cho ST, Kung HJ, Huang W, Hogenhout SA, Kuo CH. Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis. Front Microbiol 2020; 11:1531. [PMID: 32754131 PMCID: PMC7366425 DOI: 10.3389/fmicb.2020.01531] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/12/2020] [Indexed: 11/29/2022] Open
Abstract
Phytoplasmas are plant-pathogenic bacteria that impact agriculture worldwide. The commonly adopted classification system for phytoplasmas is based on the restriction fragment length polymorphism (RFLP) analysis of their 16S rRNA genes. With the increased availability of phytoplasma genome sequences, the classification system can now be refined. This work examined 11 strains in the 16SrI group within the genus ‘Candidatus Phytoplasma’ and investigated the possible species boundaries. We confirmed that the RFLP classification method is problematic due to intragenomic variation of the 16S rRNA genes and uneven weighing of different nucleotide positions. Importantly, our results based on the molecular phylogeny, differentiations in chromosomal segments and gene content, and divergence in homologous sequences, all supported that these strains may be classified into multiple operational taxonomic units (OTUs) equivalent to species. Strains assigned to the same OTU share >97% genome-wide average nucleotide identity (ANI) and >78% of their protein-coding genes. In comparison, strains assigned to different OTUs share < 94% ANI and < 75% of their genes. Reduction in homologous recombination between OTUs is one possible explanation for the discontinuity in genome similarities, and these findings supported the proposal that 95% ANI could serve as a cutoff for distinguishing species in bacteria. Additionally, critical examination of these results and the raw sequencing reads led to the identification of one genome that was presumably mis-assembled by combining two sequencing libraries built from phytoplasmas belonging to different OTUs. This finding provided a cautionary tale for working on uncultivated bacteria. Based on the new understanding of phytoplasma divergence and the current genome availability, we developed five molecular markers that could be used for multilocus sequence analysis (MLSA). By selecting markers that are short yet highly informative, and are distributed evenly across the chromosome, these markers provided a cost-effective system that is robust against recombination. Finally, examination of the effector gene distribution further confirmed the rapid gains and losses of these genes, as well as the involvement of potential mobile units (PMUs) in their molecular evolution. Future improvements on the taxon sampling of phytoplasma genomes will allow further expansions of similar analysis, and thus contribute to phytoplasma taxonomy and diagnostics.
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Affiliation(s)
- Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Jui Kung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Weijie Huang
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | | | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Dekaboruah E, Suryavanshi MV, Chettri D, Verma AK. Human microbiome: an academic update on human body site specific surveillance and its possible role. Arch Microbiol 2020; 202:2147-2167. [PMID: 32524177 PMCID: PMC7284171 DOI: 10.1007/s00203-020-01931-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/21/2022]
Abstract
Human body is inhabited by vast number of microorganisms which form a complex ecological community and influence the human physiology, in the aspect of both health and diseases. These microbes show a relationship with the human immune system based on coevolution and, therefore, have a tremendous potential to contribute to the metabolic function, protection against the pathogen and in providing nutrients and energy. However, of these microbes, many carry out some functions that play a crucial role in the host physiology and may even cause diseases. The introduction of new molecular technologies such as transcriptomics, metagenomics and metabolomics has contributed to the upliftment on the findings of the microbiome linked to the humans in the recent past. These rapidly developing technologies are boosting our capacity to understand about the human body-associated microbiome and its association with the human health. The highlights of this review are inclusion of how to derive microbiome data and the interaction between human and associated microbiome to provide an insight on the role played by the microbiome in biological processes of the human body as well as the development of major human diseases.
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Affiliation(s)
- Elakshi Dekaboruah
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, 737102, India
| | | | - Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, 737102, India
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok, Sikkim, 737102, India.
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8
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Detection of 16SrVI and 16SrIX phytoplasma groups in pot marigold and tickseed plants in northeastern Iran. Folia Microbiol (Praha) 2020; 65:697-703. [PMID: 32372278 DOI: 10.1007/s12223-020-00772-x] [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: 06/05/2019] [Accepted: 01/16/2020] [Indexed: 10/24/2022]
Abstract
Pot marigold and tickseed are ornamental plants with many medicinal and cosmetic uses and for landscape, respectively. During a survey in 2018, phyllody symptoms were observed in high percentages in these plants in some regions of the Razavi Khorasan province (northeastern Iran). Total DNA was extracted from symptomatic and asymptomatic plants and polymerase chain reaction was carried on using universal phytoplasma primer pairs P1/P7 and nested primer pairs R16F2n/R16R2. The nested amplification of 1200-bp fragments confirmed the presence of phytoplasmas only in the symptomatic plants. BLAST search, phylogenetic analysis, and virtual RFLP patterns of cloned amplicons allowed to classify the pot marigold phyllody phytoplasma in the 16SrVI-A subgroup while tickseed phyllody was enclosed in the 16SrIX-I subgroup. This is the first report of the association of a 16SrVI phytoplasma with pot marigold phyllody in Iran and of the phytoplasma presence in tickseed.
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Wulff NA, Fassini CG, Marques VV, Martins EC, Coletti DAB, Teixeira DDC, Sanches MM, Bové JM. Molecular Characterization and Detection of 16SrIII Group Phytoplasma Associated with Huanglongbing Symptoms. PHYTOPATHOLOGY 2019; 109:366-374. [PMID: 30226423 DOI: 10.1094/phyto-03-18-0081-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
When huanglongbing (HLB) was found in Brazil in 2004, 'Candidatus Liberibacter americanus' was infecting most of the trees while 'Ca. L. asiaticus' was present in a minor proportion. Currently, 'Ca. L. asiaticus' is the predominant bacterium associated with HLB in citrus trees in São Paulo (SP) and Minas Gerais (MG) States, the major citrus-growing regions in Brazil. A phytoplasma from the 16SrIX group was associated with HLB symptoms in Brazil in 2007, in plants free of Liberibacter spp. In this report, HLB samples testing negative for 'Ca. L. asiaticus', 'Ca. L. americanus', and 16SrIX phytoplasma were infected with 16SrIII phytoplasmas. Coinfection with 'Ca. L. asiaticus' and 16SrIII was also found. The 16S ribosomal RNA (rRNA) gene sequences from 22 samples were obtained and sequenced, confirming that the 16SrIII group phytoplasma is associated with HLB symptoms in SP and MG States. Ten single-nucleotide polymorphisms (SNPs) were found in the 1,427-bp 16S rRNA gene sequences from 16SrIII phytoplasmas from citrus, whereas none was detected in 16S rRNA gene sequences among 16SrIX phytoplasma from citrus. Ribosomal protein (rp) rpsSrplVrpsC gene sequences were amplified with 16SrIII group-specific primers, sequenced from a subset of nine samples, and assembled into three groups based on eight SNPs. SNPs in 16S rRNA gene and rp gene sequences are common in 16SrIII phytoplasmas from other hosts and this phytoplasma group is widespread in South America. 16SrIII phytoplasmas highly related are commonly found in Melia azedarach, a widespread tree in Brazil and Argentina. The finding of a new phytoplasma associated with HLB symptoms belonging to the 16SrIII group reinforces the need to develop diagnostic tools to assess HLB-associated microbiomes.
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Affiliation(s)
- Nelson Arno Wulff
- 1 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040 and PPG Biotecnologia, IQ/UNESP Araraquara, SP, 14800-060. Brazil
| | - Camila Giacomo Fassini
- 2 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | - Viviani Vieira Marques
- 2 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | - Elaine Cristina Martins
- 2 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | | | - Diva do Carmo Teixeira
- 2 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | | | - Joseph Marie Bové
- 2 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040, Brazil
- 4 UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, INRA, 71 avenue Edouard Bourlaux, CS20032, F-33882 Villenave d'Ornon Cedex, France
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10
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Abstract
Phytoplasma detection and identification is primarily based on PCR followed by restriction fragment length polymorphism analysis. This method detects and differentiates phytoplasmas including those not yet identified. The protocol describes the application of this method for identification of phytoplasmas at 16S rRNA (16Sr) group and 16Sr subgroup levels on amplicons and also in silico on the same sequences.
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11
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Perez-Lopez E, Vincent C, Moreau D, Hammond C, Town J, Dumonceaux TJ. A novel 'Candidatus Phytoplasma asteris' subgroup 16SrI-(E/AI)AI associated with blueberry stunt disease in eastern Canada. Int J Syst Evol Microbiol 2018; 69:322-332. [PMID: 30431416 DOI: 10.1099/ijsem.0.003100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplasmas ('Candidatus Phytoplasma' species) are phytopathogenic bacteria vectored by insects and are associated with crop diseases that cause severe yield losses by affecting reproductive tissue development. Infection of northern highbush blueberry plants (Vaccinium corymbosum; Ericaceae) with phytoplasma leads to yield losses by altering plant development resulting in stunting and subsequent plant death. Samples collected from symptomatic blueberry plants in two important blueberry-producing areas in Canada, in the provinces of Québec and Nova Scotia, were analysed for the presence of DNA sequences associated with phytoplasma. Analysis of the 16S rRNA gene sequences demonstrated that the plants were infected with a strain of 'Candidatus Phytoplasma asteris', which was previously identified as blueberry stunt phytoplasma (BBS; 16SrI-E). Examination of further bacterial sequences revealed that two distinct 16S rRNA-encoding gene sequences were present in each sample in combination with a single chaperonin-60 (cpn60) sequence and a single rpoperon sequence, suggesting that this strain displays 16S rRNA-encoding gene sequence heterogeneity. Two distinct rrnoperons, rrnE and the newly described rrnAI, were identified in samples analysed from all geographic locations. We propose, based on the sequences obtained, delineating the new subgroup 16SrI-(E/AI)AI, following the nomenclature proposed for heterogeneous subgroups. To our knowledge, this is the first report of a heterogeneous phytoplasma strain affecting blueberry plants and associated with blueberry stunt disease.
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Affiliation(s)
- Edel Perez-Lopez
- 1Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Charles Vincent
- 2Agriculture et Agroalimentaire Canada, Centre de recherche et de développement de Saint-Jean-sur-Richelieu, Québec, Canada
| | - Debra Moreau
- 3Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, Nova Scotia, Canada
| | - Christine Hammond
- 4Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
| | - Jennifer Town
- 4Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
| | - Tim J Dumonceaux
- 5Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,4Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
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12
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Pérez-López E, Dumonceaux TJ. Detection and identification of the heterogeneous novel subgroup 16SrXIII-(A/I)I phytoplasma associated with strawberry green petal disease and Mexican periwinkle virescence. Int J Syst Evol Microbiol 2016; 66:4406-4415. [DOI: 10.1099/ijsem.0.001365] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Edel Pérez-López
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de Las Culturas Veracruzanas, Xalapa, Veracruz, Mexico
| | - Tim J. Dumonceaux
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada
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13
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Mitrović J, Smiljković M, Seemüller E, Reinhardt R, Hüttel B, Büttner C, Bertaccini A, Kube M, Duduk B. Differentiation of 'Candidatus Phytoplasma cynodontis' Based on 16S rRNA and groEL Genes and Identification of a New Subgroup, 16SrXIV-C. PLANT DISEASE 2015; 99:1578-1583. [PMID: 30695967 DOI: 10.1094/pdis-01-15-0061-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
'Candidatus Phytoplasma cynodontis' is widespread in bermudagrass and has only been found in monocotyledonous plants. Molecular studies carried out on strains collected in Italy, Serbia, and Albania enabled verification of molecular variability in the 16S ribosomal RNA (rRNA) gene. Based on restriction fragment length polymorphism and sequence analyses, the strains from Serbia were clearly differentiated from all others and assigned to a new ribosomal DNA (rDNA) subgroup designated as 16SrXIV-C. A system for amplification of fragments containing the 'Ca. P. cynodontis' groEL gene was developed to enable study of its variability in related strains belonging to different 16SrXIV subgroups. Despite the fact that the groEL gene exhibited a greater sequence variation than 16S rRNA, the phylogenetic tree based on groEL gene sequence analysis was highly congruent with the 16S rDNA-based tree. The groEL gene analyses supported differentiation of the Serbian strains and definition of the new subgroup 16SrXIV-C. Phylogenetic analyses of both genes confirmed distinct phylogenetic lineages for strains belonging to 16SrXIV subgroups. Furthermore, groEL is the only nonribosomal marker developed for characterization of 'Ca. P. cynodontis' thus far, and its application in molecular surveys should provide better insight into the relationships among these phytoplasmas and correlation between strain differentiation and their geographical distribution.
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Affiliation(s)
- J Mitrović
- Laboratory of Applied Phytopathology, Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - M Smiljković
- Laboratory of Applied Phytopathology, Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Erich Seemüller
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Dossenheim, Germany
| | | | | | - Carmen Büttner
- Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Assunta Bertaccini
- DipSA, Plant Pathology, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Michael Kube
- Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Bojan Duduk
- Laboratory of Applied Phytopathology, Institute of Pesticides and Environmental Protection, Belgrade, Serbia
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Sankar SA, Lagier JC, Pontarotti P, Raoult D, Fournier PE. The human gut microbiome, a taxonomic conundrum. Syst Appl Microbiol 2015; 38:276-86. [DOI: 10.1016/j.syapm.2015.03.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/16/2023]
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15
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de Souza AN, da Silva FN, Bedendo IP, Carvalho CM. A Phytoplasma Belonging to a 16SrIII-A Subgroup and dsRNA Virus Associated with Cassava Frogskin Disease in Brazil. PLANT DISEASE 2014; 98:771-779. [PMID: 30708630 DOI: 10.1094/pdis-04-13-0440-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cassava frogskin disease (CFSD) is a particular threat in cassava because symptoms remain hidden until harvest and losses can be total. The information related to the etiological agent of this disease is contradictory, because some authors believe it is caused by phytoplasmas while others believe that it is caused by a virus. In order to refine detection protocols and to characterize organisms associated with CFSD in Brazil, 32 symptomatic and 20 asymptomatic cassava plants were collected in Minas Gerais state. Total DNA was extracted and used for nested polymerase chain reaction (PCR) to detect phytoplasmas. Because endophytic Bacillus spp. led to false positives, primers were designed to facilitate the detection of phytoplasma in the presence of bacteria. In addition, double-stranded (ds)RNA was extracted from tubers and used in reverse-transcription PCR for the detection of the RNA-dependent RNA polymerase gene from Cassava frogskin virus segment 4. The detected phytoplasma was identified as belonging to the group 16SrIII-A by restriction fragment length polymorphism (RFLP), sequencing, and RFLP in silico. This is the first report of a phytoplasma belonging to the 16SrIII-A group associated with cassava plants, the first molecular characterization of a phytoplasma associated with CFSD in Brazil, and a first report of phytoplasma and a dsRNA virus (possible reovirus) co-infecting cassava plants with CFSD symptoms.
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Affiliation(s)
| | | | - Ivan P Bedendo
- Department of Plant Pathology and Nematology, ESALQ/USP, Piracicaba, Brazil
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16
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Winks CJ, Andersen MT, Charles JG, Beever RE. Identification of Zeoliarus oppositus (Hemiptera: Cixiidae) as a Vector of 'Candidatus Phytoplasma australiense'. PLANT DISEASE 2014; 98:10-15. [PMID: 30708617 DOI: 10.1094/pdis-04-13-0421-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
'Candidatus Phytoplasma australiense' is associated with a number of plant diseases in New Zealand. The only known vector of this pathogen was Zeoliarus atkinsoni, a planthopper considered to be monophagous on New Zealand flax (Phormium spp.). The work carried out shows that Z. oppositus, which is polyphagous, is able to vector 'Ca. P. australiense' to both Coprosma robusta (karamu) and Cordyline australis (New Zealand cabbage tree). Although transmission was achieved to both these species, the disease symptomatology was more evident in C. australis. Two approaches were taken to achieve transmission. First, insects were collected from areas around symptomatic Coprosma plants and caged directly on test plants. Second, insects were collected from grasses and sedges in areas where disease was less evident and were fed on known infected Coprosma plants prior to being caged on test plants. Transmission was achieved using both approaches, although transmission was far greater (30% compared with 4%) from insects that were directly applied. Phytoplasma DNA was detected in 12% of Z. oppositus individuals tested during all the trials. This work identifies a new vector for 'Ca. P. australiense' and contributes to our understanding of the ecology of Cordyline sudden decline and Coprosma lethal decline.
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Affiliation(s)
- C J Winks
- Landcare Research, Private Bag 92170, Auckland 1142, New Zealand
| | - M T Andersen
- The New Zealand Institute for Plant & Food Research Ltd., Private Bag 92169, Victoria Street West, Auckland 1142, New Zealand
| | - J G Charles
- The New Zealand Institute for Plant & Food Research Ltd., Private Bag 92169, Victoria Street West, Auckland 1142, New Zealand
| | - R E Beever
- Landcare Research, Auckland, New Zealand
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17
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Zhao Y, Wei W, Lee IM, Shao J, Suo X, Davis RE. The iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment. Methods Mol Biol 2013; 938:329-38. [PMID: 22987428 DOI: 10.1007/978-1-62703-089-2_28] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The iPhyClassifier is an internet-based research tool for quick identification and classification of diverse phytoplasmas. The iPhyClassifier simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) patterns. Based on RFLP pattern similarity coefficient scores, the iPhyClassifier gives instant suggestions on group and subgroup classification status of the phytoplasma strains under study. The iPhyClassifier also aligns the query sequences with that of reference strains of all previously described 'Candidatus Phytoplasma' species, -calculates sequence similarity scores, and assigns the phytoplasmas under study into respective 'Ca. Phytoplasma' species as related strains according to the guidelines set forth by the Phytoplasma Taxonomy Group of the International Research Program on Comparative Mycoplasmology. Additional functions of the iPhyClassifier include delineation of potentially new phytoplasma groups and subgroups as well as new 'Ca. Phytoplasma' species. This chapter describes the program components, the operational procedure, and the underlying principles of the iPhyClassifier operation. The chapter also provides hints on how to interpret the results.
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Affiliation(s)
- Yan Zhao
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD, USA.
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18
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Abstract
Current phytoplasma detection and identification methods are primarily based on nested polymerase chain reaction followed by restriction fragment length polymorphism analysis and gel electrophoresis. These methods can potentially detect and differentiate all phytoplasmas including those previously not described. The present protocol describes the application of this method for identification of phytoplasmas at 16S rRNA (16Sr) group and 16Sr subgroup levels.
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Makarova O, Contaldo N, Paltrinieri S, Kawube G, Bertaccini A, Nicolaisen M. DNA barcoding for identification of 'Candidatus Phytoplasmas' using a fragment of the elongation factor Tu gene. PLoS One 2012; 7:e52092. [PMID: 23272216 PMCID: PMC3525539 DOI: 10.1371/journal.pone.0052092] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 11/12/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Phytoplasmas are bacterial phytopathogens responsible for significant losses in agricultural production worldwide. Several molecular markers are available for identification of groups or strains of phytoplasmas. However, they often cannot be used for identification of phytoplasmas from different groups simultaneously or are too long for routine diagnostics. DNA barcoding recently emerged as a convenient tool for species identification. Here, the development of a universal DNA barcode based on the elongation factor Tu (tuf) gene for phytoplasma identification is reported. METHODOLOGY/PRINCIPAL FINDINGS We designed a new set of primers and amplified a 420-444 bp fragment of tuf from all 91 phytoplasmas strains tested (16S rRNA groups -I through -VII, -IX through -XII, -XV, and -XX). Comparison of NJ trees constructed from the tuf barcode and a 1.2 kbp fragment of the 16S ribosomal gene revealed that the tuf tree is highly congruent with the 16S rRNA tree and had higher inter- and intra- group sequence divergence. Mean K2P inter-/intra- group divergences of the tuf barcode did not overlap and had approximately one order of magnitude difference for most groups, suggesting the presence of a DNA barcoding gap. The use of the tuf barcode allowed separation of main ribosomal groups and most of their subgroups. Phytoplasma tuf barcodes were deposited in the NCBI GenBank and Q-bank databases. CONCLUSIONS/SIGNIFICANCE This study demonstrates that DNA barcoding principles can be applied for identification of phytoplasmas. Our findings suggest that the tuf barcode performs as well or better than a 1.2 kbp fragment of the 16S rRNA gene and thus provides an easy procedure for phytoplasma identification. The obtained sequences were used to create a publicly available reference database that can be used by plant health services and researchers for online phytoplasma identification.
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Affiliation(s)
- Olga Makarova
- Department of Agroecology, AU Science and Technology, Aarhus University, Slagelse, Denmark
| | - Nicoletta Contaldo
- Alma Mater Studiorum, University of Bologna, DipSA – Plant Pathology, Bologna, Italy
| | - Samanta Paltrinieri
- Alma Mater Studiorum, University of Bologna, DipSA – Plant Pathology, Bologna, Italy
| | - Geofrey Kawube
- Department of Agroecology, AU Science and Technology, Aarhus University, Slagelse, Denmark
| | - Assunta Bertaccini
- Alma Mater Studiorum, University of Bologna, DipSA – Plant Pathology, Bologna, Italy
| | - Mogens Nicolaisen
- Department of Agroecology, AU Science and Technology, Aarhus University, Slagelse, Denmark
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20
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Rodríguez-Blanco A, Vetion G, Escande ML, Delille D, Ghiglione JF. Gallaecimonas pentaromativorans gen. nov., sp. nov., a bacterium carrying 16S rRNA gene heterogeneity and able to degrade high-molecular-mass polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 2010; 60:504-509. [DOI: 10.1099/ijs.0.013532-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped, halotolerant bacterium, designated strain CEE_131T, which degraded high-molecular-mass polycyclic aromatic hydrocarbons of four and five rings, was isolated from intertidal sediment of Corcubion Ria in Cee, A Coruña, Spain. Direct sequencing showed ambiguities and suggested heterogeneity. Cloned 16S rRNA gene sequence PCR products yielded five different sequences varying at five positions. Strain CEE_131T showed rather distant relationships to its phylogenetically closest neighbours, including the genera Rheinheimera and Serratia, exhibiting 91 % sequence similarity with Rheinheimera perlucida BA131T and Serratia proteamaculans subsp. quinovora DSM 4597T. The major fatty acids were C16 : 1
ω7c, C16 : 0 and C18 : 1
ω7c. The DNA G+C content was 41.7 mol%. On the basis of these distinct phenotypic and genotypic characteristics, strain CEE_131T is considered to represent a novel species in a new genus in the class Gammaproteobacteria, for which the name Gallaecimonas pentaromativorans gen. nov., sp. nov. is proposed. The type strain is CEE_131T (=DSM 21945T=CECT 7479T).
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Affiliation(s)
- Arturo Rodríguez-Blanco
- CNRS, UMR7621, Laboratoire d'Océanographie Biologique de Banyuls, Avenue Fontaulé, BP44, F-66650 Banyuls-sur-Mer, France
- UPMC Univ Paris 06, UMR 7621, Laboratoire ARAGO, Avenue Fontaulé, BP44, F-66650 Banyuls-sur-Mer, France
| | - Gilles Vetion
- CNRS, UMR7621, Laboratoire d'Océanographie Biologique de Banyuls, Avenue Fontaulé, BP44, F-66650 Banyuls-sur-Mer, France
- UPMC Univ Paris 06, UMR 7621, Laboratoire ARAGO, Avenue Fontaulé, BP44, F-66650 Banyuls-sur-Mer, France
| | - Marie-Line Escande
- CNRS, UMR7621, Laboratoire d'Océanographie Biologique de Banyuls, Avenue Fontaulé, BP44, F-66650 Banyuls-sur-Mer, France
- UPMC Univ Paris 06, UMR 7621, Laboratoire ARAGO, Avenue Fontaulé, BP44, F-66650 Banyuls-sur-Mer, France
| | - Daniel Delille
- CNRS, UMR7621, Laboratoire d'Océanographie Biologique de Banyuls, Avenue Fontaulé, BP44, F-66650 Banyuls-sur-Mer, France
- UPMC Univ Paris 06, UMR 7621, Laboratoire ARAGO, Avenue Fontaulé, BP44, F-66650 Banyuls-sur-Mer, France
| | - Jean-François Ghiglione
- CNRS, UMR7621, Laboratoire d'Océanographie Biologique de Banyuls, Avenue Fontaulé, BP44, F-66650 Banyuls-sur-Mer, France
- UPMC Univ Paris 06, UMR 7621, Laboratoire ARAGO, Avenue Fontaulé, BP44, F-66650 Banyuls-sur-Mer, France
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Zhao Y, Wei W, Lee IM, Shao J, Suo X, Davis RE. Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII). Int J Syst Evol Microbiol 2009; 59:2582-93. [PMID: 19622670 PMCID: PMC2884932 DOI: 10.1099/ijs.0.010249-0] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplasmas, the causal agents of numerous plant diseases, are insect-vector-transmitted, cell-wall-less bacteria descended from ancestral low-G+C-content Gram-positive bacteria in the Bacillus-Clostridium group. Despite their monophyletic origin, widely divergent phytoplasma lineages have evolved in adaptation to specific ecological niches. Classification and taxonomic assignment of phytoplasmas have been based primarily on molecular analysis of 16S rRNA gene sequences because of the inaccessibility of measurable phenotypic characters suitable for conventional microbial characterization. In the present study, an interactive online tool, iPhyClassifier, was developed to expand the efficacy and capacity of the current 16S rRNA gene sequence-based phytoplasma classification system. iPhyClassifier performs sequence similarity analysis, simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) profiles. Based on calculated RFLP pattern similarity coefficients and overall sequence similarity scores, iPhyClassifier makes instant suggestions on tentative phytoplasma 16Sr group/subgroup classification status and 'Candidatus Phytoplasma' species assignment. Using iPhyClassifier, we revised and updated the classification of strains affiliated with the peach X-disease phytoplasma group. The online tool can be accessed at http://www.ba.ars.usda.gov/data/mppl/iPhyClassifier.html.
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Affiliation(s)
- Yan Zhao
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA.
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22
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Liew PWY, Jong BC, Goh CM, Ahmad M. Bacterial diversity associated with empty oil palm fruit bunch compost as revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes. J GEN APPL MICROBIOL 2009; 55:233-40. [PMID: 19590151 DOI: 10.2323/jgam.55.233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Pauline Woan Ying Liew
- Agrotechnology and Bioscience Division, Malaysian Nuclear Agency (Nuclear Malaysia), Bangi, 43000 Kajang, Selangor Darul Ehsan, Malaysia
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Wei W, Lee IM, Davis RE, Suo X, Zhao Y. Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages. Int J Syst Evol Microbiol 2008; 58:2368-77. [DOI: 10.1099/ijs.0.65868-0] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Cai H, Wei W, Davis RE, Chen H, Zhao Y. Genetic diversity among phytoplasmas infecting Opuntia species: virtual RFLP analysis identifies new subgroups in the peanut witches'-broom phytoplasma group. Int J Syst Evol Microbiol 2008; 58:1448-57. [DOI: 10.1099/ijs.0.65615-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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Wei W, Davis RE, Lee IM, Zhao Y. Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups. Int J Syst Evol Microbiol 2007; 57:1855-1867. [PMID: 17684271 DOI: 10.1099/ijs.0.65000-0] [Citation(s) in RCA: 261] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the CLUSTAL_X program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative 'Candidatus Phytoplasma' taxa.
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Affiliation(s)
- Wei Wei
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Robert E Davis
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Ing-Ming Lee
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Yan Zhao
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
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26
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Noreen F, Akbergenov R, Hohn T, Richert-Pöggeler KR. Distinct expression of endogenous Petunia vein clearing virus and the DNA transposon dTph1 in two Petunia hybrida lines is correlated with differences in histone modification and siRNA production. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 50:219-229. [PMID: 17444906 DOI: 10.1071/ap06016] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Endogenous viruses exist in all kingdoms. They usually have active mechanisms of integration, as in bacteriophage lambda and animal retroviruses, and sophisticated mechanisms to maintain a proviral state over decades and generations. Plant para retroviruses, however, neither have an integrase, nor genes for maintaining the proviral state. How are those elements controlled, and under what conditions can they be activated? Here we study the proviral state of endogenous petunia vein clearing virus (ePVCV). Our results support the hypothesis that the proviral state is associated with a host silencing mechanism manifested by DNA methylation, chromatin modification and production of small interfering (si) RNAs. PVCV may be induced by applying abiotic stress, leading to the development of viral symptoms and increased transcript and siRNA levels. Similar levels of ePVCV DNA methylation were observed in two different lines of Petunia hybrida, RdC (rose du ciel) and W138, the latter known for its active version of transposon dTph1. In contrast, significant differences in histone modification were detected. The predominant association of ePVCV sequences with histone H3 methylated at lysine 9 (H3mK9) in RdC and with about equal amounts of H3mK9 and H3mK4 in W138 indicates a less repressive proviral state in the latter cultivar.
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Affiliation(s)
- Faiza Noreen
- Friedrich Miescher Institute, Maulbeerstlasse 66, CH-4058 Basel, Switzerland
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27
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Vickery MCL, Nilsson WB, Strom MS, Nordstrom JL, DePaola A. A real-time PCR assay for the rapid determination of 16S rRNA genotype in Vibrio vulnificus. J Microbiol Methods 2007; 68:376-84. [PMID: 17070612 DOI: 10.1016/j.mimet.2006.02.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 02/09/2006] [Indexed: 10/24/2022]
Abstract
In a terminal restriction fragment polymorphism (T-RFLP) study, we recently reported a significant association between the type B 16S rRNA gene and clinical strains of Vibrio vulnificus associated with the consumption of raw oysters. In the present study we describe a real-time PCR assay for the rapid determination of the 16S rRNA type of V. vulnificus isolates. This assay was used to reexamine the 16S rRNA gene type in the strains studied previously by T-RFLP and additional isolates from selected sources. Analyses revealed that 15 of the strains (10 environmental and 5 clinical) previously found to be 16S rRNA type A actually appear to possess both the type A and B genes. The presence of both alleles was confirmed by cloning and sequencing both gene types from one strain. To our knowledge, this is the first report of 16S rRNA sequence heterogeneity within individual strains of V. vulnificus. The findings confirm the T-RFLP data that 16S rRNA type may be a useful marker for determining the clinical significance of V. vulnificus in disease in humans and cultured eels. The real-time PCR assay is much more rapid and less resource-intensive than T-RFLP, and should facilitate further study of the occurrence and distribution of the 16S rRNA genotypes of V. vulnificus. These studies should provide more definitive estimates of the risks associated with this organism and may lead to a better understanding of its virulence mechanism(s).
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Affiliation(s)
- Michael C L Vickery
- Gulf Coast Seafood Laboratory, U. S. Food and Drug Administration, Dauphin Island, Alabama 36528, United States.
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28
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Andersen MT, Newcomb RD, Liefting LW, Beever RE. Phylogenetic Analysis of "Candidatus Phytoplasma australiense" Reveals Distinct Populations in New Zealand. PHYTOPATHOLOGY 2006; 96:838-845. [PMID: 18943748 DOI: 10.1094/phyto-96-0838] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT The phytoplasma "Candidatus Phytoplasma australiense" has been reported from New Zealand and Australia, where it has been associated with a range of host plants, especially since the 1970s. Partial tuf gene sequences of 36 New Zealand (NZ) isolates from four different host genera revealed nine different variants, which clustered into two distinct groups without any obvious correlation with host or geographic region. Phylogenetic analysis of these sequences, together with those available from Australian isolates, revealed three distinct clades: one found solely in Australia, one found solely in NZ, and a third with representatives from both countries. These divisions are consistent with differences observed in the 16-23S rRNA internal transcribed spacer region; therefore, we conclude that they represent three distinct subgroups: tuf 1, tuf 2, and tuf 3. We estimated a time of divergence for the three clades based on a synonymous substitution rate calculated by comparing the complete tuf gene sequence from the Loofah witches'-broom phytoplasma and "Candidatus Phytoplasma australiense". Using a calibration date of 110 million years, the estimated time to a common ancestor for all clades (6 to 9 million years ago) suggests divergence during the Miocene, well after the geological separation of NZ and Australia.
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29
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Olivier A, Lee HY, Côté JC. Study of the heterogeneity of 16S rRNA genes in gamma-proteobacteria: implications for phylogenetic analysis. J GEN APPL MICROBIOL 2006; 51:395-405. [PMID: 16474200 DOI: 10.2323/jgam.51.395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Audrey Olivier
- Département de Génie Biologique, Institut Universitaire de Technologie, Université d'Angers, France
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30
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DYET K, MARTIN D. Clonal analysis of the serogroup B meningococci causing New Zealand's epidemic. Epidemiol Infect 2006; 134:377-83. [PMID: 16490143 PMCID: PMC2870387 DOI: 10.1017/s0950268805004954] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2005] [Indexed: 11/07/2022] Open
Abstract
An epidemic of meningococcal disease caused by serogroup B meningococci expressing the P1.7-2,4 PorA protein began in New Zealand in 1991. The PorA type has remained stable. Different porB have been found in association with the P1.7-2,4 PorA, although type 4 has been most common. The clonal origins of B:P1.7-2,4 meningococci isolated from cases during 1990 to the end of 2003 were analysed. In 1990, the year immediately preceding the recognized increase in disease rates, all three subclones (ST-41, ST-42, and ST-154) of the ST-41/44 clonal complex occurred among the five isolates of B:P1.7-2,4. The two sequence types, ST-42 and ST-154, continued to cause most disease throughout New Zealand. Isolates belonging to subclone ST-41 were mostly identified early in the epidemic and in the South Island. 16S rRNA typing indicated that isolates belonging to the subclones ST-41 and ST-154 share a common ancestor, with those typing as ST-42 more distantly related with some genetically ambiguous. It is possible that ST-41 and ST-154 may have evolved one from the other but evolution to ST-42 is more difficult to explain. It is possible that one or more of the ST types could have been introduced into New Zealand prior to the first detection of clinical cases in 1990. Genetic diversity may have occurred during carriage in the community.
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Affiliation(s)
- K. H. DYET
- Communicable Disease Group, Institute of Environmental Science and Research, Porirua, New Zealand
| | - D. R. MARTIN
- Communicable Disease Group, Institute of Environmental Science and Research, Porirua, New Zealand
- Author for correspondence: Dr D. R. Martin, Communicable Disease Group, Institute of Environmental Science and Research, PO Box 50 348, Porirua, New Zealand. ()
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'Candidatus Phytoplasma', a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects. Int J Syst Evol Microbiol 2005; 54:1243-1255. [PMID: 15280299 DOI: 10.1099/ijs.0.02854-0] [Citation(s) in RCA: 227] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The trivial name 'phytoplasma' has been adopted to collectively name wall-less, non-helical prokaryotes that colonize plant phloem and insects, which were formerly known as mycoplasma-like organisms. Although phytoplasmas have not yet been cultivated in vitro, phylogenetic analyses based on various conserved genes have shown that they represent a distinct, monophyletic clade within the class Mollicutes. It is proposed here to accommodate phytoplasmas within the novel genus 'Candidatus (Ca.) Phytoplasma'. Given the diversity within 'Ca. Phytoplasma', several subtaxa are needed to accommodate organisms that share <97.5% similarity among their 16S rRNA gene sequences. This report describes the properties of 'Ca. Phytoplasma', a taxon that includes the species 'Ca. Phytoplasma aurantifolia' (the prokaryote associated with witches'-broom disease of small-fruited acid lime), 'Ca. Phytoplasma australiense' (associated with Australian grapevine yellows), 'Ca. Phytoplasma fraxini' (associated with ash yellows), 'Ca. Phytoplasma japonicum' (associated with Japanese hydrangea phyllody), 'Ca. Phytoplasma brasiliense' (associated with hibiscus witches'-broom in Brazil), 'Ca. Phytoplasma castaneae' (associated with chestnut witches'-broom in Korea), 'Ca. Phytoplasma asteris' (associated with aster yellows), 'Ca. Phytoplasma mali' (associated with apple proliferation), 'Ca. Phytoplasma phoenicium' (associated with almond lethal disease), 'Ca. Phytoplasma trifolii' (associated with clover proliferation), 'Ca. Phytoplasma cynodontis' (associated with Bermuda grass white leaf), 'Ca. Phytoplasma ziziphi' (associated with jujube witches'-broom), 'Ca. Phytoplasma oryzae' (associated with rice yellow dwarf) and six species-level taxa for which the Candidatus species designation has not yet been formally proposed (for the phytoplasmas associated with X-disease of peach, grapevine flavescence dorée, Central American coconut lethal yellows, Tanzanian lethal decline of coconut, Nigerian lethal decline of coconut and loofah witches'-broom, respectively). Additional species are needed to accommodate organisms that, despite their 16S rRNA gene sequence being >97.5% similar to those of other 'Ca. Phytoplasma' species, are characterized by distinctive biological, phytopathological and genetic properties. These include 'Ca. Phytoplasma pyri' (associated with pear decline), 'Ca. Phytoplasma prunorum' (associated with European stone fruit yellows), 'Ca. Phytoplasma spartii' (associated with spartium witches'-broom), 'Ca. Phytoplasma rhamni' (associated with buckthorn witches'-broom), 'Ca. Phytoplasma allocasuarinae' (associated with allocasuarina yellows), 'Ca. Phytoplasma ulmi' (associated with elm yellows) and an additional taxon for the stolbur phytoplasma. Conversely, some organisms, despite their 16S rRNA gene sequence being <97.5% similar to that of any other 'Ca. Phytoplasma' species, are not presently described as Candidatus species, due to their poor overall characterization.
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Zhang J, Hogenhout SA, Nault LR, Hoy CW, Miller SA. Molecular and symptom analyses of phytoplasma strains from lettuce reveal a diverse population. PHYTOPATHOLOGY 2004; 94:842-849. [PMID: 18943104 DOI: 10.1094/phyto.2004.94.8.842] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT Epidemics of aster yellows in lettuce in Ohio are caused by at least seven distinct phytoplasma strains in the aster yellows (AY) group. Five of the strains are newly reported: AY-BW, AY-WB, AY-BD3, AY-SS, and AY-SG. All seven strains were characterized based on symptoms in aster and lettuce, and by polymerase chain reaction (PCR). Strain AY-BD2 (formerly 'Bolt') causes yellowing and leaf distortion in lettuce and bolting in aster, whereas strain AY-S (formerly 'Severe') causes stunting, leaf clustering, and phyllody. Strain AY-WB causes yellowing and wilting in lettuce and witches'-broom in aster. Strain AY-SG induces horizontal growth in lettuce and aster plants. Strain AY-BW causes chlorosis of emerging leaves and abnormally upright growth of leaf petioles. AY-SS causes symptoms similar to those caused by AY-S but has a different PCR-restriction fragment length polymorphism (RFLP) banding pattern. Strains AY-BD2 and AY-BD-3 cause mild leaf and stem distortion in lettuce but are differentiated by PCR-RFLP. All phytoplasma strains collected from lettuce in Ohio belong to the 16SrI group. AY-WB belongs to the 16SrI-A subgroup and the other six belong to the 16SrI-B subgroup. Five of the seven strains were distinguished from each other by primer typing. The results of phylogenetic analyses of sequences of the 16S rRNA genes were basically consistent with the classification based on PCR-RFLP, in which AY-WB clustered with phytoplasmas of the 16rIA subgroup and the other Ohio lettuce strains clustered with phytoplasmas in the 16SrI-B subgroup.
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Candelon B, Guilloux K, Ehrlich SD, Sorokin A. Two distinct types of rRNA operons in the Bacillus cereus group. MICROBIOLOGY-SGM 2004; 150:601-611. [PMID: 14993309 DOI: 10.1099/mic.0.26870-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Bacillus cereus group includes insecticidal bacteria (B. thuringiensis), food-borne pathogens (B. cereus and B. weihenstephanensis) and B. anthracis, the causative agent of anthrax. The precise number of rRNA operons in 12 strains of the B. cereus group was determined. Most of the tested strains possess 13 operons and the tested psychrotolerant strains contain 14 operons, the highest number ever found in bacteria. The separate clustering of the tested psychrotolerant strains was confirmed by partial sequencing of several genes distributed over the chromosomes. Analysis of regions downstream of the 23S rRNA genes in the type strain B. cereus ATCC 14579 indicates that the rRNA operons can be divided into two classes, I and II, consisting respectively of eight and five operons. Class II operons exhibit multiple tRNA genes downstream of the 5S rRNA gene and a putative promoter sequence in the 23S-5S intergenic region, suggesting that 5S rRNA and the downstream tRNA genes can be transcribed independently of the 16S and 23S genes. Similar observations were made in the recently sequenced genome of B. anthracis strain Ames. The existence of these distinct types of rRNA operons suggests an unknown mechanism for regulation of rRNA and tRNA synthesis potentially related to the pool of amino acids available for protein synthesis.
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MESH Headings
- Bacillus cereus/classification
- Bacillus cereus/genetics
- Base Sequence
- DNA, Bacterial/genetics
- Genes, Bacterial
- Molecular Sequence Data
- Operon
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- Ribotyping
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Benjamin Candelon
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas cedex, France
| | - Kévin Guilloux
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas cedex, France
| | - S Dusko Ehrlich
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas cedex, France
| | - Alexei Sorokin
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas cedex, France
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Chang KF, Hwang SF, Khadhair AH, Kawchuk L, Howard R. Detection and molecular characterization of an aster yellows phytoplasma in poker statice and Queen Anne's lace in Alberta, Canada. Microbiol Res 2004; 159:43-50. [PMID: 15160606 DOI: 10.1016/j.micres.2004.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Queen Anne's lace and poker statice plants were found with a yellows-type disease with typical phytoplasma symptoms in an experimental farm near Brooks, Alberta in 1996. Phytoplasma bodies were detected by transmission electron microscopy in phloem cells of symptomatic plants, but not in healthy plants. The presence of a phytoplasma was confirmed by analysis with the polymerase chain reaction. Using a pair of universal primer sequences derived from phytoplasma 16S rRNA, an amplified product of the expected size (1.2 kb) was observed in samples from infected plants, but not in asymptomatic plants. Sequence analysis of the PCR products from the 16S/23S rDNA intergenic spacer region indicated that the two phytoplasma isolates in Queen Anne's lace and poker statice are genetically closely related to the western aster yellows phytoplasma.
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MESH Headings
- Alberta
- Base Sequence
- DNA, Bacterial/analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/analysis
- DNA, Ribosomal/isolation & purification
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/isolation & purification
- Daucus carota/microbiology
- Daucus carota/ultrastructure
- Genes, rRNA
- Microscopy, Electron
- Molecular Sequence Data
- Phytoplasma/genetics
- Phytoplasma/isolation & purification
- Plant Diseases/microbiology
- Plumbaginaceae/microbiology
- Plumbaginaceae/ultrastructure
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Kan-Fa Chang
- Field Crop Development Centre, 6000 C and E Trail, Lacombe, Alta., Canada T4L 1W1
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35
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Davis RE, Jomantiene R, Kalvelyte A, Dally EL. Differential amplification of sequence heterogeneous ribosomal RNA genes and classification of the 'Fragaria multicipita' phytoplasma. Microbiol Res 2003; 158:229-36. [PMID: 14521232 DOI: 10.1078/0944-5013-00201] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ribosomal (r) RNA interoperon sequence heterogeneity in the 'Fragaria multicipita' phytoplasma, a member of group 16SrVI, was initially observed in RFLP patterns of rDNA amplified in the polymerase chain reaction (PCR), and was confirmed through sequence analysis of cloned rDNA. Sequences from operons rrnA and rrnB were amplified in PCR primed by primer pair P1/P7 but from only rrnA in PCR primed by primer pair R16mF2/R16mR1. Preferential amplification of DNA from operon rrnA was explained by base mismatches between the R16mF2/R16mR1 primers and primer annealing sites in rrnB. The results revealed potential for classification of a phytoplasma into two different subgroups within a 16S rRNA group, if the phytoplasma's 16S rRNA gene sequences are independently characterized. It is suggested that the rRNA operon containing species-specific signature sequence(s) should be specified, and where possible sequences from both 16S rRNA genes should be included, in descriptions of new 'Candidatus Phytoplasma species'.
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Affiliation(s)
- Robert E Davis
- Molecular Plant Pathology Laboratory, Plant Sciences Institute, Agricultural Research Service-USDA, Beltsville, MD 20705, USA.
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36
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Marchandin H, Teyssier C, Siméon de Buochberg M, Jean-Pierre H, Carriere C, Jumas-Bilak E. Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: implications for phylogeny and taxonomy. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1493-1501. [PMID: 12777489 DOI: 10.1099/mic.0.26132-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Among the seven species characterized within the genus Veillonella, three (Veillonella dispar, Veillonella parvula and Veillonella atypica) have so far been isolated from human flora and during infectious processes. Sequencing and analysis of 16S rDNA (rrs) has been described as the best method for identification of Veillonella strains at the species level since phenotypic characteristics are unable to differentiate between species. rrs sequencing for the three species isolated from humans showed more than 98 % identity between them. Four rrs copies were found in the reference strains and in all the clinical isolates studied. The sequences of each rrs were determined for the clinical strain ADV 360.1, and they showed a relatively high level of heterogeneity (1.43 %). In the majority of cases, polymorphic positions corresponded to nucleotides allowing differentiation between the three species isolated from humans. Moreover, variability observed between rrs copies was higher than that between 16S rDNA sequences of V. parvula and V. dispar. Phylogenetic analysis showed that polymorphism between rrs copies affected the position of strain ADV 360.1 in the tree. Variable positions occurred in stems and loops belonging to variable and hypervariable regions of the 16S rRNA secondary structure but did not change the overall structure of the 16S rRNA. PCR-RFLP experiments performed on 27 clinical isolates of Veillonella sp. suggested that inter-rrs heterogeneity occurs widely among the members of the genus VEILLONELLA: These results, together with the lack of phenotypic criteria for species differentiation, give preliminary arguments for unification of V. dispar and V. parvula.
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MESH Headings
- Base Sequence
- Chromosomes, Bacterial/genetics
- DNA, Bacterial/genetics
- DNA, Ribosomal/genetics
- Gene Dosage
- Genes, Bacterial
- Genetic Variation
- Humans
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- Species Specificity
- Veillonella/classification
- Veillonella/genetics
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Affiliation(s)
- Hélène Marchandin
- Service de Bactériologie, Hôpital Arnaud de Villeneuve, 34295 Montpellier Cedex 5, France
| | - Corinne Teyssier
- Laboratoire de Bactériologie, Faculté de Pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Michèle Siméon de Buochberg
- Laboratoire de Bactériologie, Faculté de Pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Hélène Jean-Pierre
- Service de Bactériologie, Hôpital Arnaud de Villeneuve, 34295 Montpellier Cedex 5, France
| | - Christian Carriere
- Service de Bactériologie, Hôpital Arnaud de Villeneuve, 34295 Montpellier Cedex 5, France
| | - Estelle Jumas-Bilak
- Laboratoire de Bactériologie, Faculté de Pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
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37
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Seo PS, Yokota A. The phylogenetic relationships of cyanobacteria inferred from 16S rRNA, gyrB, rpoC1 and rpoD1 gene sequences. J GEN APPL MICROBIOL 2003; 49:191-203. [PMID: 12949700 DOI: 10.2323/jgam.49.191] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Phylogenetic analysis of cyanobacteria was carried out using the small subunit rRNA (16S rRNA), DNA gyrase subunit B (gyrB), DNA-dependent RNA polymerase gamma subunit (rpoC1) and a principal sigma factor of E. coli sigma(70) type for DNA-dependent RNA polymerase (rpoD1) gene sequences of 24 strains which contained 5 subgroups of cyanobacteria-3 strains of the Chroococcales, 5 strains of the Pluerocapsales, 7 strains of the Oscillatoriales, 7 strains of the Nostocales and 2 strains of the Stigonematales. Degenerated PCR primers of gyrB, rpoC1 and rpoD1 genes were designed using consensus amino acid sequences registered in GenBank. The phylogenetic positions of cyanobacteria were resolved through phylogenetic analysis based on 16S rDNA, gyrB, rpoC1 and rpoD1 gene sequences. Phylogenies of gyrB, rpoC1 and rpoD1 support 16S rRNA-based classification of cyanobacteria. Interestingly, phylogenies from amino acid sequences deduced from gyrB and combined amino acid sequences deduced from rpoC1 and rpoD1 genes strongly support that of 16S rRNA, but the branching pattens of the trees based on 16S rDNA, GyrB, rpoC1, rpoD1 and combined amino acid sequences deduced from rpoC1 and rpoD1 were not congruent. In this study, we showed the correlation among phylogenetic relationships of 16S rDNA, gyrB, rpoC1 and rpoD1 genes. The phylogenetic trees based on the sequences of 16S rDNA, GyrB, rpoC1, rpoD1 and the combined amino acid sequences deduced from rpoC1 and rpoD1 showed that the lateral gene transfer of rRNA might be suspected for Synechocystis sp. PCC 6803.
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Affiliation(s)
- Pil-Soo Seo
- Laboratory of Bioresources, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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38
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Teyssier C, Marchandin H, Siméon De Buochberg M, Ramuz M, Jumas-Bilak E. Atypical 16S rRNA gene copies in Ochrobactrum intermedium strains reveal a large genomic rearrangement by recombination between rrn copies. J Bacteriol 2003; 185:2901-9. [PMID: 12700269 PMCID: PMC154400 DOI: 10.1128/jb.185.9.2901-2909.2003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ochrobactrum intermedium is an opportunistic human pathogen belonging to the alpha 2 subgroup of proteobacteria. The 16S rDNA sequences of nine O. intermedium isolates from a collection of clinical and environmental isolates exhibited a 46-bp insertion at position 187, which was present in only one sequence among the 82 complete or partial 16S rDNA sequences of Ochrobactrum spp. available in data banks. Reverse transcription-PCR experiments showed that the 46-bp insertion remained in the 16S rRNA. The inserted sequence folded into a stem-loop structure, which took place in and prolonged helix H184 of the 16S rRNA molecule. Helix H184 has been described as conserved in length among eubacteria, suggesting the idiosyncratic character of the 46-bp insertion. Pulsed-field gel electrophoresis experiments showed that seven of the clinical isolates carrying the 46-bp insertion belonged to the same clone. Insertion and rrn copy numbers were determined by hybridization and I-CeuI digestion. In the set of clonal isolates, the loss of two insertion copies revealed the deletion of a large genomic fragment of 150 kb, which included one rrn copy; deletion occurred during the in vivo evolution of the clone. Determination of the rrn skeleton suggested that the large genomic rearrangement occurred during events involving homologous recombination between rrn copies. The loss of insertion copies suggested a phenomenon of concerted evolution among heterogeneous rrn copies.
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Affiliation(s)
- Corinne Teyssier
- Laboratoire de Bactériologie, Faculté de Pharmacie, Montpellier, France
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39
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Khadhair AH, Evans IR, Choban B. Identification of aster yellows phytoplasma in garlic and green onion by PCR-based methods. Microbiol Res 2003; 157:161-7. [PMID: 12398284 DOI: 10.1078/0944-5013-00146] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the summer of 1999, typical yellows-type symptoms were observed on garlic and green onion plants in a number of gardens and plots around Edmonton, Alberta, Canada. DNA was extracted from leaf tissues of evidently healthy and infected plants. DNA amplifications were conducted on these samples, using two primer pairs, R16F2n/R2 and R16(1)F1/R1, derived from phytoplasma rDNA sequences. DNA samples of aster yellows (AY), lime witches'-broom (LWB) and potato witches'-broom (PWB) phytoplasmas served as controls and were used to determine group relatedness. In a direct polymerase chain reaction (PCR) assay, DNA amplification with universal primer pair R16F2n/R2 gave the expected amplified products of 1.2 kb. Dilution (1/40) of each of the latter products were used as template and nested with specific primer pair R16(1)F1/R1. An expected PCR product of 1.1 kb was obtained from each phytoplasma-infected garlic and green onion samples, LWB and AY phytoplasmas but not from PWB phytoplasma. An aliquot from each amplification product (1.2 kb) with universal primers was subjected to PCR-based restriction fragment length polymorphism (RFLP) to identify phytoplasma isolates, using four restriction endonucleases (AluI, KpnI, MseI and RsaI). DNA amplification with specific primer pair R16(1)F1/R1 and RFLP analysis indicated the presence of AY phytoplasma in the infected garlic and green onion samples. These results suggest that AY phytoplasma in garlic and green onion samples belong to the subgroup 16Sr1-A.
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40
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Jung HY, Miyata SI, Oshima K, Kakizawa S, Nishigawa H, Wei W, Suzuki S, Ugaki M, Hibi T, Namba S. First complete nucleotide sequence and heterologous gene organization of the two rRNA operons in the phytoplasma genome. DNA Cell Biol 2003; 22:209-15. [PMID: 12804119 DOI: 10.1089/104454903321655837] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phytoplasmas are cell-wallless Gram-positive low G + C bacteria belonging to the Mollicutes that inhabit the cytoplasm of plants and insects. Although phytoplasmas possess two ribosomal RNA (rrn) operons, only one has been fully sequenced. Here, we determined the complete nucleotide sequence of both rrn operons (designated rrnA and rrnB) of onion yellows (OY) phytoplasma. Both operons have rRNA genes organized as 5'-16S-23S-5S-3' with very highly conserved sequences; the 16S, 23S, and 5S rRNA genes are 99.9, 99.8, and 99.1% identical between the two operons. However, the organization of tRNA genes in the upstream region from 16S rRNA gene and in the downstream region from 5S rRNA gene differs markedly. Several promoter candidates were detected upstream from both operons, which suggests that both operons are functional. Interestingly, both have a tRNA(Ile) gene in the 16S-23S spacer region, while the reported rrnB operon of loofah witches' broom phytoplasma does not, indicating heterogenous gene organization of rrnB within phytoplasmas. The phytoplasma tRNA gene organization is similar to that of acholeplasmas, a closely related mollicute, and different from that of mycoplasmas, another mollicute. Moreover, the organization suggests that the rrn operons were derived from that of a related nonmollicute bacterium, Bacillus subtilis. This data should shed light on the evolutionary relationships and phylogeny of the mollicutes.
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MESH Headings
- Acholeplasmataceae/genetics
- Base Sequence
- Blotting, Southern
- Cloning, Molecular
- Conserved Sequence
- DNA, Intergenic
- Gene Order
- Genes, rRNA
- Genome, Bacterial
- Gram-Positive Bacteria/genetics
- Molecular Sequence Data
- Phylogeny
- Promoter Regions, Genetic
- RNA, Ribosomal
- RNA, Ribosomal, 16S
- RNA, Ribosomal, 23S
- RNA, Ribosomal, 5S
- RNA, Transfer/genetics
- Sequence Analysis, DNA
- Sequence Analysis, RNA
- rRNA Operon
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Affiliation(s)
- Hee-Young Jung
- Division of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku. Tokyo 113-8657, Japan
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Sacchi CT, Whitney AM, Reeves MW, Mayer LW, Popovic T. Sequence diversity of Neisseria meningitidis 16S rRNA genes and use of 16S rRNA gene sequencing as a molecular subtyping tool. J Clin Microbiol 2002; 40:4520-7. [PMID: 12454145 PMCID: PMC154644 DOI: 10.1128/jcm.40.12.4520-4527.2002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2002] [Revised: 08/28/2002] [Accepted: 09/20/2002] [Indexed: 11/20/2022] Open
Abstract
We investigated the diversity of the primary sequences of 16S rRNA genes among Neisseria meningitidis strains (Men) and evaluated the use of this approach as a molecular subtyping tool. We aligned and compared a 1,417-bp fragment of the 16S rRNA gene from 264 Men strains of serogroups A, B, C, and Y (MenA, MenB, MenC, and MenY, respectively) isolated throughout the world over a 30-year period. Thirty-one positions of difference were found among 49 16S types: differences between types ranged from 1 to 14 positions (0.07 to 0.95%). 16S types and serogroups were highly associated; only 3 out 49 16S types were shared by two or more serogroups. We have identified 16S types that are exclusively associated with strains of certain hypervirulent clones: 16S type 5 with MenA subgroup III, 16S type 4 with the MenB electrophoretic type 5 (ET-5) complex, and 16S types 12 and 13 with MenC of the ET-37 complex. For MenC strains, 16S sequencing provided the highest sensitivity and specificity and the best overall association with the outbreak-related versus sporadic isolates when compared with pulsed-field gel electrophoresis, multilocus enzyme electrophoresis, and multilocus sequence typing. We demonstrated for the first time an unexpected diversity among 16S rRNA genes of Men strains, identified 16S types associated with well-defined hypervirulent clones, and showed the potential of this approach to rapidly identify virulent strains associated with outbreaks and/or an increased incidence of sporadic disease.
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Affiliation(s)
- Claudio T Sacchi
- Meningitis and Special Pathogens Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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42
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Friedrich U, Prior K, Altendorf K, Lipski A. High bacterial diversity of a waste gas-degrading community in an industrial biofilter as shown by a 16S rDNA clone library. Environ Microbiol 2002; 4:721-34. [PMID: 12460280 DOI: 10.1046/j.1462-2920.2002.00349.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The bacterial diversity of an industrial biofilter used for waste gas abatement in an animal-rendering plant was investigated. A 16S rDNA clone library was generated and 444 clones were screened using computer-aided amplified ribosomal DNA restriction analysis (ARDRA). Of the screened clones, 60.8% showed unique ARDRA patterns and the remaining 174 clones were clustered into 65 groups. Almost full-length 16S rDNA sequences of 106 clones were determined and 90.5% of the clones were affiliated with the two phyla Proteobacteria and Bacteroidetes. Alpha-, Beta-, and Gammaproteobacteria accounted for 22.1, 17.6 and 18.6% respectively. Minor portions were affiliated with the Actinobacteria (2.0%), Firmicutes and Verrucomicrobia (both 1.0%), and the Deltaproteobacteria and Thermomicrobia (each 0.5%). Only six out of the 106 16S rDNA sequences exhibited similarities of more than 97% to classified bacterial species indicating that a substantial fraction of the clone sequences were derived from unknown taxa. It was also evaluated whether a database containing 281 computer-simulated bacterial rDNA fragment patterns generated from published reference sequences can be used for identification purposes. The data analysis demonstrated that this was possible only for a small number of clones, which were closely related to described bacterial strains. Rarefaction analysis of ARDRA clusters demonstrated that the 444 clones screened are insufficient to describe the entire diversity of the clone library.
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Affiliation(s)
- Udo Friedrich
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, Germany.
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Sacchi CT, Whitney AM, Mayer LW, Morey R, Steigerwalt A, Boras A, Weyant RS, Popovic T. Sequencing of 16S rRNA gene: a rapid tool for identification of Bacillus anthracis. Emerg Infect Dis 2002; 8:1117-23. [PMID: 12396926 PMCID: PMC2730316 DOI: 10.3201/eid0810.020391] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In a bioterrorism event, a tool is needed to rapidly differentiate Bacillus anthracis from other closely related spore-forming Bacillus species. During the recent outbreak of bioterrorism-associated anthrax, we sequenced the 16S rRNA generom these species to evaluate the potential of 16S rRNA gene sequencing as a diagnostic tool. We found eight distinct 16S types among all 107 16S rRNA gene seqs fuences that differed from each other at 1 to 8 positions (0.06% to 0.5%). All 86 B. anthracis had an identical 16S gene sequence, designated type 6; 16S type 10 was seen in all B. thuringiensis strains; six other 16S types were found among the 10 B. cereus strains. This report describes the first demonstration of an exclusive association of a distinct 16S sequence with B. anthracis. Consequently, we were able to rapidly identify suspected isolates and to detect the B. anthracis 16S rRNA gene directly from culture-negative clinical specimens from seven patients with laboratory-confirmed anthrax.
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Affiliation(s)
- Claudio T Sacchi
- Centers for Desease Control and Prevention , Atlanta, Georgia 30333, USA.
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Khadhair AH, Tewari JP, Howard RJ, Paul VH. Detection of aster yellows phytoplasma in false flax based on PCR and RFLP. Microbiol Res 2002; 156:179-84. [PMID: 11572458 DOI: 10.1078/0944-5013-00100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
False flax (Camelina sativa L.) plants were found to be infected with a yellows-type disease caused by a phytoplasma in experimental plots at the Edmonton Research station. Alberta, Canada. Typical phytoplasmas were detected in the phloem cells in ultrathin sections from leaf midrib tissues examined by electron microscopy. These observations were supported by polymerase chain reaction (PCR) using two primer pairs, R16 F2n/R2 and R16(1)F1/R1, derived from phytoplasma rDNA sequences. Aster yellows (AY) and potato witches'-broom (PWB) phytoplasma DNA samples served as controls and were used to study group relatedness. In a direct PCR assay, DNA amplification with universal primer pair R16F2n/R2 gave the expected PCR products of 1.2 kb. Based on a nested-PCR assay using the latter PCR products as templates, and a specific primer pair, R16(1)F1/R1, designed on the basis of AY phytoplasma rDNA sequences, a PCR product of 1.1 kb was obtained from each phytoplasma-infected false flax and AY sample, but not from PWB phytoplasma and healthy controls. DNA amplification with specific primer pair R16(1)F1/R1 and restriction fragment length polymorphism indicated the presence of AY phytoplasma in the infected false flax sample. This is the first reported characterization of AY phytoplasma in false flax.
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Iteman I, Rippka R, Tandeau de Marsac N, Herdman M. rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira. MICROBIOLOGY (READING, ENGLAND) 2002; 148:481-496. [PMID: 11832512 DOI: 10.1099/00221287-148-2-481] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The taxonomic coherence and phylogenetic relationships of 11 planktonic heterocystous cyanobacterial isolates were examined by investigating two areas of the rRNA operon, the 16S rRNA gene (rrnS) and the internal transcribed spacer (ITS) located between the 16S rRNA and 23S rRNA genes. The rrnS sequences were determined for five strains, including representatives of Anabaena flos-aquae, Aphanizomenon flos-aquae, Nodularia sp. and two alkaliphilic planktonic members of the genera Anabaenopsis and Cyanospira, whose phylogenetic position was previously unknown. Comparison of the data with those previously published for individual groups of planktonic heterocystous cyanobacteria showed that, with the exception of members assigned to the genus Cylindrospermopsis, all the planktonic strains form a distinct subclade within the monophyletic clade of heterocystous cyanobacteria. Within this subclade five different phylogenetic clusters were distinguished. The phylogenetic groupings of Anabaena and Aphanizomenon strains within three of these clusters were not always consistent with their generic or specific assignments based on classical morphological definitions, and the high degree of sequence similarity between strains of Anabaenopsis and Cyanospira suggests that they may be assignable to a single genus. Ribotyping and additional studies performed on PCR amplicons of the 16S rDNA or the ITS for the 11 planktonic heterocystous strains demonstrated that they all contain multiple rrn operons and ITS regions of variable size. Finally, evidence is provided for intra-genomic sequence heterogeneity of the 16S rRNA genes within most of the individual isolates.
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Affiliation(s)
- Isabelle Iteman
- Unité des Cyanobactéries (CNRS URA 2172), Département de Biochimie et Génétique Moléculaire, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France1
| | - Rosmarie Rippka
- Unité des Cyanobactéries (CNRS URA 2172), Département de Biochimie et Génétique Moléculaire, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France1
| | - Nicole Tandeau de Marsac
- Unité des Cyanobactéries (CNRS URA 2172), Département de Biochimie et Génétique Moléculaire, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France1
| | - Michael Herdman
- Unité des Cyanobactéries (CNRS URA 2172), Département de Biochimie et Génétique Moléculaire, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France1
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Andersen MT, Beever RE, Sutherland PW, Forster RLS. Association of "Candidatus Phytoplasma australiense" with Sudden Decline of Cabbage Tree in New Zealand. PLANT DISEASE 2001; 85:462-469. [PMID: 30823120 DOI: 10.1094/pdis.2001.85.5.462] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sudden decline of the New Zealand cabbage tree (Cordyline australis) results in the rapid death of affected plants within months of first external symptoms becoming apparent. Symptoms, which have been observed in saplings and mature trees, include vascular discoloration and leaf yellowing followed by leaf desiccation and eventual plant collapse. Previous work failed to link the disease with any causal agent. A phytoplasma has now been detected in all symptomatic saplings and some symptomatic trees tested, using one-step and nested polymerase chain reaction (PCR) to amplify portions of the 16S rRNA gene. This phytoplasma was not detected in nonsymptomatic plants. Phytoplasma DNA was found in shoot and rhizome apices, leaves and wood tissue of saplings, and in the rhizome apex and trunk tissues of adult trees. Sequencing of the PCR products from selected samples indicated that the phytoplasma is "Candidatus Phytoplasma australiense." Phytoplasma cells were detected by transmission electron microscopy in phloem sieve tubes of the rhizomes of affected saplings. One sapling with early symptoms recovered after injection with tetracycline antibiotic, but two saplings with advanced symptoms did not recover. It is concluded that "Candidatus Phytoplasma australiense" is present in symptomatic plants and is the cause of sudden decline.
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Affiliation(s)
- Mark T Andersen
- The Horticulture and Food Research Institute of New Zealand Ltd., Private Bag 92169, Auckland, New Zealand
| | - Ross E Beever
- Landcare Research, Private Bag 92170, Auckland, New Zealand
| | - Paul W Sutherland
- The Horticulture and Food Research Institute of New Zealand Ltd., Private Bag 92169, Auckland, New Zealand
| | - Richard L S Forster
- The Horticulture and Food Research Institute of New Zealand Ltd., Private Bag 92169, Auckland, New Zealand
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Abstract
During the past decade, research has yielded new knowledge about the plant and insect host ranges, geographical distribution, and phylogenetic relationships of phytoplasmas, and a taxonomic system has emerged in which distinct phytoplasmas are named as separate "Candidatus phytoplasma species." In large part, this progress has resulted from the development and use of molecular methods to detect, identify, and classify phytoplasmas. While these advances continue, research has recently begun on the phytoplasma genome, how phytoplasmas cause disease, the role of mixed phytoplasmal infections in plant diseases, and molecular/genetic phenomena that underlie symptom development in plants. These and other recent advances are laying the foundation for future progress in understanding the mechanisms of phytoplasma pathogenicity, organization of the phytoplasma genome, evolution of new phytoplasma strains and emergence of new diseases, bases of insect transmissibility and specificity of transmission, and plant gene expression in response to phytoplasmal infection, as well as the design of novel approaches to achieve effective control of phytoplasmal diseases.
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Affiliation(s)
- I M Lee
- United States Department of Agriculture, Molecular Plant Pathology Laboratory, and Insect Biocontrol Laboratory, Agricultural Research Service, Beltsville, Maryland 20705, USA.
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Khadhair AH, Evans IR. Molecular and microscopical detection of aster yellows phytoplasma associated with infected parsnip. Microbiol Res 2000; 155:53-7. [PMID: 10830901 DOI: 10.1016/s0944-5013(00)80023-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Typical phytoplasma yellows symptoms were observed in parsnip (Pastinaca sativa L.) plants grown around Edmonton, Alberta, Canada. Examination of ultrathin sections of leaf midribs by electron microscopy revealed numerous phytoplasma bodies localized in the phloem cells. DNA extracted from the infected leaves was amplified with a 16S rDNA universal primer pair P1/P6 giving the expected PCR product of 1.5 kb. The phytoplasma was confirmed as a member of the aster yellows (AY) group by amplification with the specific primer pair R16(1)/F1/R1 that was designed on the basis of AY phytoplasma 16S rDNA sequences. In the nested PCR assays, the expected DNA fragment of 1.1 kb was amplified with this specific primer set. Similar restriction patterns were found for the 1.1 kb PCR products of the phytoplasma isolated from parsnip and an AY phytoplasma control after digestion with restriction endonucleases AluI, HhaI, KpnI and RsaI. This is the first reported observation of aster yellows in parsnip in Canada.
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Janson S, Bergman B, Carpenter EJ, Giovannoni SJ, Vergin K. Genetic analysis of natural populations of the marine diazotrophic cyanobacterium Trichodesmium. FEMS Microbiol Ecol 1999. [DOI: 10.1111/j.1574-6941.1999.tb00635.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Yap WH, Zhang Z, Wang Y. Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol 1999; 181:5201-9. [PMID: 10464188 PMCID: PMC94023 DOI: 10.1128/jb.181.17.5201-5209.1999] [Citation(s) in RCA: 209] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe here the presence of two distinct types of rRNA operons in the genome of a thermophilic actinomycete Thermomonospora chromogena. The genome of T. chromogena contains six rRNA operons (rrn), of which four complete and two incomplete ones were cloned and sequenced. Comparative analysis revealed that the operon rrnB exhibits high levels of sequence variations to the other five nearly identical ones throughout the entire length of the operon. The coding sequences for the 16S and 23S rRNA genes differ by approximately 6 and 10%, respectively, between the two types of operons. Normal functionality of rrnB is concluded on the basis of the nonrandom distribution of nucleotide substitutions, the presence of compensating nucleotide covariations, the preservation of secondary and tertiary rRNA structures, and the detection of correctly processed rRNAs in the cell. Comparative sequence analysis also revealed a close evolutionary relationship between rrnB operon of T. chromogena and rrnA operon of another thermophilic actinomycete Thermobispora bispora. We propose that T. chromogena acquired rrnB operon from T. bispora or a related organism via horizontal gene transfer.
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MESH Headings
- Actinomycetales/classification
- Actinomycetales/genetics
- Base Sequence
- Blotting, Southern
- Cloning, Molecular
- DNA, Bacterial
- DNA, Ribosomal/analysis
- Evolution, Molecular
- Gene Amplification
- Gene Expression
- Genetic Variation
- Genome, Bacterial
- Molecular Sequence Data
- Nucleic Acid Conformation
- Polymerase Chain Reaction
- RNA, Bacterial
- RNA, Ribosomal, 16S
- Sequence Analysis, DNA
- rRNA Operon
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Affiliation(s)
- W H Yap
- Microbial Collection and Screening Laboratory, Institute of Molecular and Cell Biology, National University of Singapore, Singapore 117609
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