Publications by authors named "Bevan S Weir"

19 Publications

  • Page 1 of 1

Antimicrobial Metabolites against Methicillin-Resistant from the Endophytic Fungus .

Molecules 2021 Feb 19;26(4). Epub 2021 Feb 19.

Bioluminescent Superbugs Lab, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.

Antimicrobial bioassay-guided fractionation of the endophytic fungi led to the isolation of a new unsymmetrical naphthoquinone dimer, neofusnaphthoquinone B (), along with four known natural products (-). Structure elucidation was conducted by nuclear magnetic resonance (NMR) spectroscopic methods, and the antimicrobial activity of all the natural products was investigated, revealing to be moderately active towards methicillin-resistant (MRSA) with a minimum inhibitory concentration (MIC) of 16 µg/mL.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/molecules26041094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7922810PMC
February 2021

gcType: a high-quality type strain genome database for microbial phylogenetic and functional research.

Nucleic Acids Res 2021 01;49(D1):D694-D705

Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkaa957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778895PMC
January 2021

A Revised Structure and Assigned Absolute Configuration of Theissenolactone A.

Molecules 2020 Oct 20;25(20). Epub 2020 Oct 20.

Bioluminescent Superbugs Lab, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.

Antimicrobial bioassay-guided fractionation of led to the isolation of a γ-lactone with a furo[3,4-]pyran-5-one bicyclic ring system () and three known compounds, (3,4)-4-hydroxymellein (), (3,4)-4-hydroxymellein () and 7-hydroxy-3-(1-hydroxyethyl)isobenzofuran-1(3)-one (). Structure elucidation was conducted by NMR spectroscopic methods. Absolute configuration of (2, 3, 5, 7 8) was established using the chiral derivatizing agent MPA and was fully supported by calculated specific rotation and ECD spectra. The spectroscopic data observed for were identical to those previously reported for theissenolactone A (), necessitating a correction of the latter (from C-5/C-8 ring fusion to ). Compounds - were evaluated for antimicrobial activity against a panel of pathogens.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/molecules25204823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7587954PMC
October 2020

Molecular Evolution of Type III Secreted Effector Proteins.

Front Plant Sci 2019 5;10:418. Epub 2019 Apr 5.

Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada.

Diverse Gram-negative pathogens like employ type III secreted effector (T3SE) proteins as primary virulence factors that combat host immunity and promote disease. T3SEs can also be recognized by plant hosts and activate an effector triggered immune (ETI) response that shifts the interaction back toward plant immunity. Consequently, T3SEs are pivotal in determining the virulence potential of individual strains, and ultimately help to restrict pathogens to a subset of potential hosts that are unable to recognize their repertoires of T3SEs. While a number of effector families are known to be present in the species complex, one of the most persistent challenges has been documenting the complex variation in T3SE contents across a diverse collection of strains. Using the entire pan-genome of 494 strains isolated from more than 100 hosts, we conducted a global analysis of all known and putative T3SEs. We identified a total of 14,613 putative T3SEs, 4,636 of which were unique at the amino acid level, and show that T3SE repertoires of different strains vary dramatically, even among strains isolated from the same hosts. We also find substantial diversification within many T3SE families, and in many cases find strong signatures of positive selection. Furthermore, we identify multiple gene gain and loss events for several families, demonstrating an important role of horizontal gene transfer (HGT) in the evolution of T3SEs. These analyses provide insight into the evolutionary history of T3SEs as they co-evolve with the host immune system, and dramatically expand the database of T3SEs alleles.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2019.00418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460904PMC
April 2019

Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex.

Genome Biol 2019 01 3;20(1). Epub 2019 Jan 3.

Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., ESC 4041, Toronto, ON, M5S 3B2, Canada.

Background: Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crops. We examine the evolutionary relationships of 391 agricultural and environmental strains using whole-genome sequencing and evolutionary genomic analyses.

Results: We describe the phylogenetic distribution of all 77,728 orthologous gene families in the pan-genome, reconstruct the core genome phylogeny using the 2410 core genes, hierarchically cluster the accessory genome, identify the diversity and distribution of type III secretion systems and their effectors, predict ecologically and evolutionary relevant loci, and establish the molecular evolutionary processes operating on gene families. Phylogenetic and recombination analyses reveals that the species complex is subdivided into primary and secondary phylogroups, with the former primarily comprised of agricultural isolates, including all of the well-studied P. syringae strains. In contrast, the secondary phylogroups include numerous environmental isolates. These phylogroups also have levels of genetic diversity typically found among distinct species. An analysis of rates of recombination within and between phylogroups revealed a higher rate of recombination within primary phylogroups than between primary and secondary phylogroups. We also find that "ecologically significant" virulence-associated loci and "evolutionarily significant" loci under positive selection are over-represented among loci that undergo inter-phylogroup genetic exchange.

Conclusions: While inter-phylogroup recombination occurs relatively rarely, it is an important force maintaining the genetic cohesion of the species complex, particularly among primary phylogroup strains. This level of genetic cohesion, and the shared plant-associated niche, argues for considering the primary phylogroups as a single biological species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-018-1606-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317194PMC
January 2019

Genome Sequence of the Saprophytic Ascomycete Strain ICMP 19927, Isolated from New Zealand.

Genome Announc 2017 Jun 15;5(24). Epub 2017 Jun 15.

School of Biological Sciences, University of Auckland, Auckland, New Zealand.

is a common mitosporic fungus of the Didymellaceae (Ascomycota) family known for the production of numerous secondary metabolites. Here, we present the 34.7-Mbp draft genome sequence of strain ICMP 19927 assembled from a range of short-insert and long-insert Illumina libraries.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/genomeA.00557-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473283PMC
June 2017

Chemical formation of hybrid di-nitrogen calls fungal codenitrification into question.

Sci Rep 2016 12 15;6:39077. Epub 2016 Dec 15.

Dept. of Marine Sciences, University of Connecticut, Groton, Connecticut, USA.

Removal of excess nitrogen (N) can best be achieved through denitrification processes that transform N in water and terrestrial ecosystems to di-nitrogen (N) gas. The greenhouse gas nitrous oxide (NO) is considered an intermediate or end-product in denitrification pathways. Both abiotic and biotic denitrification processes use a single N source to form NO. However, N can be formed from two distinct N sources (known as hybrid N) through biologically mediated processes of anammox and codenitrification. We questioned if hybrid N produced during fungal incubation at neutral pH could be attributed to abiotic nitrosation and if NO was consumed during N formation. Experiments with gas chromatography indicated N was formed in the presence of live and dead fungi and in the absence of fungi, while NO steadily increased. We used isotope pairing techniques and confirmed abiotic production of hybrid N under both anoxic and 20% O atmosphere conditions. Our findings question the assumptions that (1) NO is an intermediate required for N formation, (2) production of N and NO requires anaerobiosis, and (3) hybrid N is evidence of codenitrification and/or anammox. The N cycle framework should include abiotic production of N.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep39077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5157039PMC
December 2016

Recommendations for competing sexual-asexually typified generic names in Sordariomycetes (except Diaporthales, Hypocreales, and Magnaporthales).

IMA Fungus 2016 Jun 8;7(1):131-53. Epub 2016 Jun 8.

Center of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.

With the advance to one scientific name for each fungal species, the generic names in the class Sordariomycetes typified by sexual and asexual morphs are evaluated based on their type species to determine if they compete with each other for use or protection. Recommendations are made for which of the competing generic names should be used based on criteria such as priority, number of potential names changes, and frequency of use. Some recommendations for well-known genera include Arthrinium over Apiospora, Colletotrichum over Glomerella, Menispora over Zignoëlla, Microdochium over Monographella, Nigrospora over Khuskia, and Plectosphaerella over Plectosporium. All competing generic names are listed in a table of recommended names along with the required action. If priority is not accorded to sexually typified generic names after 2017, only four names would require formal protection: Chaetosphaerella over Oedemium, Diatrype over Libertella, Microdochium over Monographella, and Phaeoacremonium over Romellia and Togninia. Concerning species in the recommended genera, one replacement name (Xylaria benjaminii nom. nov.) is introduced, and the following new combinations are made: Arthrinium sinense, Chloridium caesium, C. chloroconium, C. gonytrichii, Corollospora marina, C. parvula, C. ramulosa, Juncigena fruticosae, Melanospora simplex, Seimatosporium massarina, Sporoschisma daemonoropis, S. taitense, Torpedospora mangrovei, Xylaria penicilliopsis, and X. termiticola combs. nov.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5598/imafungus.2016.07.01.08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941682PMC
June 2016

Phytopathogen Genome Announcement: Draft Genome Sequences of 62 Pseudomonas syringae Type and Pathotype Strains.

Mol Plant Microbe Interact 2016 Apr 17;29(4):243-6. Epub 2016 Mar 17.

1 Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada;

Pseudomonas syringae is a diverse species-complex that includes many important crop pathogens. Here, we report the draft genomes of 62 type and pathotype strains, which provide a genomic reference for the diversity of this species complex and will contribute to the elucidation of the genomic basis of pathogenicity and host specificity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/MPMI-01-16-0013-TADOI Listing
April 2016

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Authors:
Conrad L Schoch Barbara Robbertse Vincent Robert Duong Vu Gianluigi Cardinali Laszlo Irinyi Wieland Meyer R Henrik Nilsson Karen Hughes Andrew N Miller Paul M Kirk Kessy Abarenkov M Catherine Aime Hiran A Ariyawansa Martin Bidartondo Teun Boekhout Bart Buyck Qing Cai Jie Chen Ana Crespo Pedro W Crous Ulrike Damm Z Wilhelm De Beer Bryn T M Dentinger Pradeep K Divakar Margarita Dueñas Nicolas Feau Katerina Fliegerova Miguel A García Zai-Wei Ge Gareth W Griffith Johannes Z Groenewald Marizeth Groenewald Martin Grube Marieka Gryzenhout Cécile Gueidan Liangdong Guo Sarah Hambleton Richard Hamelin Karen Hansen Valérie Hofstetter Seung-Beom Hong Jos Houbraken Kevin D Hyde Patrik Inderbitzin Peter R Johnston Samantha C Karunarathna Urmas Kõljalg Gábor M Kovács Ekaphan Kraichak Krisztina Krizsan Cletus P Kurtzman Karl-Henrik Larsson Steven Leavitt Peter M Letcher Kare Liimatainen Jian-Kui Liu D Jean Lodge Janet Jennifer Luangsa-ard H Thorsten Lumbsch Sajeewa S N Maharachchikumbura Dimuthu Manamgoda María P Martín Andrew M Minnis Jean-Marc Moncalvo Giuseppina Mulè Karen K Nakasone Tuula Niskanen Ibai Olariaga Tamás Papp Tamás Petkovits Raquel Pino-Bodas Martha J Powell Huzefa A Raja Dirk Redecker J M Sarmiento-Ramirez Keith A Seifert Bhushan Shrestha Soili Stenroos Benjamin Stielow Sung-Oui Suh Kazuaki Tanaka Leho Tedersoo M Teresa Telleria Dhanushka Udayanga Wendy A Untereiner Javier Diéguez Uribeondo Krishna V Subbarao Csaba Vágvölgyi Cobus Visagie Kerstin Voigt Donald M Walker Bevan S Weir Michael Weiß Nalin N Wijayawardene Michael J Wingfield J P Xu Zhu L Yang Ning Zhang Wen-Ying Zhuang Scott Federhen

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

Diverse honeydew-consuming fungal communities associated with scale insects.

PLoS One 2013 26;8(7):e70316. Epub 2013 Jul 26.

Centre for Microbial Innovation, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.

Sooty mould fungi are ubiquitous, abundant consumers of insect-honeydew that have been little-studied. They form a complex of unrelated fungi that coexist and compete for honeydew, which is a chemically complex resource. In this study, we used scanning electron microscopy in combination with T-RFLP community profiling and ITS-based tag-pyrosequencing to extensively describe the sooty mould community associated with the honeydews of two ecologically important New Zealand coelostomidiid scale insects, Coelostomidia wairoensis and Ultracoelostoma brittini. We tested the influence of host plant on the community composition of associated sooty moulds, and undertook limited analyses to examine the influence of scale insect species and geographic location. We report here a previously unknown degree of fungal diversity present in this complex, with pyrosequencing detecting on average 243 operational taxonomic units across the different sooty mould samples. In contrast, T-RFLP detected only a total of 24 different "species" (unique peaks). Nevertheless, both techniques identified similar patterns of diversity suggesting that either method is appropriate for community profiling. The composition of the microbial community associated with individual scale insect species varied although the differences may in part reflect variation in host preference and site. Scanning electron microscopy visualised an intertwined mass of fungal hyphae and fruiting bodies in near-intact physical condition, but was unable to distinguish between the different fungal communities on a morphological level, highlighting the need for molecular research. The substantial diversity revealed for the first time by pyrosequencing and our inability to identify two-thirds of the diversity to further than the fungal division highlights the significant gap in our knowledge of these fungal groups. This study provides a first extensive look at the community diversity of the fungal community closely associated with the keystone insect-honeydew systems of New Zealand's native forests and suggests there is much to learn about sooty mould communities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0070316PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724830PMC
April 2014

Rhizobia with 16S rRNA and nifH similar to Mesorhizobium huakuii but Novel recA, glnII, nodA and nodC genes are symbionts of New Zealand Carmichaelinae.

PLoS One 2012 31;7(10):e47677. Epub 2012 Oct 31.

Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand.

New Zealand became geographically isolated about 80 million years ago and this separation gave rise to a unique native flora including four genera of legume, Carmichaelia, Clianthus and Montigena in the Carmichaelinae clade, tribe Galegeae, and Sophora, tribe Sophoreae, sub-family Papilionoideae. Ten bacterial strains isolated from NZ Carmichaelinae growing in natural ecosystems grouped close to the Mesorhizobium huakuii type strain in relation to their 16S rRNA and nifH gene sequences. However, the ten strains separated into four groups on the basis of their recA and glnII sequences: all groups were clearly distinct from all Mesorhizobium type strains. The ten strains separated into two groups on the basis of their nodA sequences but grouped closely together in relation to nodC sequences; all nodA and nodC sequences were novel. Seven strains selected and the M. huakuii type strain (isolated from Astragalus sinicus) produced functional nodules on Carmichaelia spp., Clianthus puniceus and A. sinicus but did not nodulate two Sophora species. We conclude that rhizobia closely related to M. huakuii on the basis of 16S rRNA and nifH gene sequences, but with variable recA and glnII genes and novel nodA and nodC genes, are common symbionts of NZ Carmichaelinae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0047677PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485278PMC
May 2013

The amsterdam declaration on fungal nomenclature.

IMA Fungus 2011 Jun 7;2(1):105-12. Epub 2011 Jun 7.

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal, E-28040 Madrid, Spain; and Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, UK;

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5598/imafungus.2011.02.01.14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317370PMC
June 2011

'Candidatus Liberibacter solanacearum', associated with plants in the family Solanaceae.

Int J Syst Evol Microbiol 2009 Sep 20;59(Pt 9):2274-6. Epub 2009 Jul 20.

Plant Health and Environment Laboratory, MAF Biosecurity New Zealand, PO Box 2095, Auckland 1140, New Zealand.

A liberibacter (isolate NZ082226) was detected in a symptomatic tomato plant and subsequently in five other members of the family Solanaceae: capsicum, potato, tamarillo, cape gooseberry and chilli. Phylogenetic analyses of the 16S rRNA gene sequence, the deduced amino acid sequence of the rplJ gene and a partial nucleotide sequence of the beta operon indicated that isolate NZ082226 represents a novel candidate species of 'Candidatus Liberibacter', for which the name 'Candidatus Liberibacter solanacearum' is proposed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijs.0.007377-0DOI Listing
September 2009

A New 'Candidatus Liberibacter' Species Associated with Diseases of Solanaceous Crops.

Plant Dis 2009 Mar;93(3):208-214

Plant Health and Environment Laboratory, MAF Biosecurity New Zealand, P.O. Box 2095, Auckland 1140, New Zealand.

A new disease of glasshouse-grown tomato and pepper in New Zealand has resulted in plant decline and yield loss. Affected plants are characterized by spiky, chlorotic apical growth, curling or cupping of the leaves, and overall stunting. Transmission electron microscopy revealed the presence of phloem-limited bacterium-like organisms in symptomatic plants. The strategy used to identify the bacterium involved using specific prokaryote polymerase chain reaction (PCR) primers in combination with universal 16S rRNA primers. Sequence analysis of the 16S rRNA gene, the 16S/23S rRNA spacer region, and the rplKAJL-rpoBC operon revealed that the bacterium shared high identity with 'Candidatus Liberibacter' species. Phylogenetic analysis showed that the bacterium is distinct from the three citrus liberibacter species previously described and has been named 'Candidatus Liberibacter solanacearum'. This is the first report of a liberibacter naturally infecting a host outside the Rutaceae family. A specific PCR primer pair was developed for its detection.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-93-3-0208DOI Listing
March 2009

Isolation and characterization of microsatellite loci from Lochmaea suturalis, the heather beetle (Coleoptera: Chrysomelidae), a pest in Europe and a biocontrol agent in New Zealand.

Mol Ecol Resour 2009 Mar 31;9(2):594-6. Epub 2009 Jan 31.

Landcare Research, Private Bag 92170 Auckland 1142, New Zealand.

The heather beetle Lochmaea suturalis which is native to northwest Europe has been released as a biocontrol agent for heather in New Zealand. We have isolated and optimized eight microsatellite loci from New Zealand beetles. These loci provide markers with high polymorphism ranging from four to 20 alleles per locus. Observed heterozygosity averaged 0.631 per locus. These results suggest the markers are useful for population studies that will contribute to assessment of L. suturalis as a biocontrol agent.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1755-0998.2008.02448.xDOI Listing
March 2009

Unexpectedly diverse Mesorhizobium strains and Rhizobium leguminosarum nodulate native legume genera of New Zealand, while introduced legume weeds are nodulated by Bradyrhizobium species.

Appl Environ Microbiol 2004 Oct;70(10):5980-7

Landcare Research, Private Bag 92170, Auckland, New Zealand.

The New Zealand native legume flora are represented by four genera, Sophora, Carmichaelia, Clianthus, and Montigena. The adventive flora of New Zealand contains several legume species introduced in the 19th century and now established as serious invasive weeds. Until now, nothing has been reported on the identification of the associated rhizobia of native or introduced legumes in New Zealand. The success of the introduced species may be due, at least in part, to the nature of their rhizobial symbioses. This study set out to address this issue by identifying rhizobial strains isolated from species of the four native legume genera and from the introduced weeds: Acacia spp. (wattles), Cytisus scoparius (broom), and Ulex europaeus (gorse). The identities of the isolates and their relationship to known rhizobia were established by comparative analysis of 16S ribosomal DNA, atpD, glnII, and recA gene sequences. Maximum-likelihood analysis of the resultant data partitioned the bacteria into three genera. Most isolates from native legumes aligned with the genus Mesorhizobium, either as members of named species or as putative novel species. The widespread distribution of strains from individual native legume genera across Mesorhizobium spp. contrasts with previous reports implying that bacterial species are specific to limited numbers of legume genera. In addition, four isolates were identified as Rhizobium leguminosarum. In contrast, all sequences from isolates from introduced weeds aligned with Bradyrhizobium species but formed clusters distinct from existing named species. These results show that native legume genera and these introduced legume genera do not have the same rhizobial populations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.70.10.5980-5987.2004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC522066PMC
October 2004

Diversity of 16S rDNA sequences of Rhizobium spp. implications for species determinations.

FEMS Microbiol Lett 2004 Sep;238(1):125-31

Landcare Research, Private Bag 92170, Auckland, New Zealand.

Comparative analysis of 70 16S rDNA sequences representing 20 Rhizobium species (including pathogenic Agrobacterium spp.) was conducted using Maximum Likelihood to establish relationships of species using multiple sequences. There is no significant internal division of the Rhizobium clade to suggest that it represents more than one genus. Plant pathogenic (Agrobacterium) species are distributed within the genus. The analysis supported the synonymy of some species (Rhizobium gallicum and Rhizobium mongolense) and the need for comparative investigations of the tumorigenic and nodulating properties of Rhizobium tropici and Rhizobium rhizogenes. Misidentification of some sequences may conceal one or more putative novel species. Some sequences appear to be misidentified because of faulty sequencing or incomplete or inadequate analysis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.femsle.2004.07.026DOI Listing
September 2004