Landcare Research - Manaaki Whenua

Landcare-Research -Manaaki Whenua

Bevan Weir

Bevan Weir
Position: Researcher
Team: Systematics
Location: Auckland
Private Bag 92170
Auckland Mail Centre
Auckland 1142
Phone: +64 9 574 4115
Fax: +64 3 321 9998

Contact Bevan

Research Interests

Research Interests

My research field is the systematics and phylogenetics of fungi and bacteria. I work on a diverse range of organisms, such as bacteria, fungi and chromists for different clients or projects, however many of the techniques, applications, and skills are common across taxa. 

I am particularly interested in symbiosis and pathogenicity between microorganisms and their hosts, my PhD was on a group symbiotic nitrogen-fixing plant bacteria “rhizobia”, and my postdoc was on a group of plant pathogenic fungi “Colletotrichum”. Systematics (taxonomy and nomenclature) have played a large role in my research projects, and I have a good knowledge of the respective nomenclatural codes of Bacteria and Fungi. 

I actively use the latest phylogenetic applications and theory, including species-tree delimitations for refining species concepts in Colletotrichum. One of the most popular pages on my personal website is a tutorial on the use of model testing software in analysing DNA sequences. 

Genomics is becoming a large part of my research activities, for my previous two contract reports for MPI Biosecurity NZ I have sequenced and analysed bacterial genomes to obtain a robust identification as well as identify determinants of pathogenicity and sub-specific strain differences. 

I am curator of one of New Zealand’s “nationally significant” collections, the ICMP collection of 20,000 living cryopreserved fungi and bacteria. This resource is used extensively for biosecurity, taxonomic, and plant pathogenic research by the NZ and international research community, and recently I have begun to use the collection to discover useful bioactive compounds, for example we have a bacterium that produces a peptide antimicrobial that is very specific in killing the Psa disease affecting kiwifruit in New Zealand. I also conduct contract and consulting work for local biotechnology companies that produce novel biological fungicides and insecticides that have lower environmental impacts than traditional chemical compounds.

Publications

Qualifications

Qualifications

  • Auckland
    PhD Biological Sciences
    2007
  • Auckland
    BTech (Hons) Biotechnology
    2002

Publications

Publications

  • Shirouzu T, Hosaka K, Nam K-O, Weir BS, Johnston PR, Hosoya T 2017. Phylogenetic relationships of eight new Dacrymycetes collected from New Zealand. Persoonia 38: 156-169. http://doi.org/10.3767/003158517X695280 (Journal Article, 2017)
  • Fokin M, Fleetwood D, Weir BS, Villas-Boas S 2017. Genome sequence of the saprophytic ascomycete Epicoccum nigrum strain ICMP 19927, isolated from New Zealand. Genome Announcements 5(24): e00557-17. https://doi.org/10.1128/genomeA.00557-17 (Journal Article, 2017)
  • Lopes-Santos L, Castro DBA, Ferreira-Tonin M, Corrêa DBA, Weir BS, Park D, Ottoboni LMM, Neto JR, Destéfano SAL 2017. Reassessment of the taxonomic position of Burkholderia andropogonis and description of Robbsia andropogonis gen. nov., comb. nov. Antonie van Leeuwenhoek 110(6): 727-736. http://dx.doi.org/10.1007/s10482-017-0842-6 (Journal Article, 2017)
  • Johnston PR, Weir BS, Cooper JA 2017. Open data on fungi and bacterial plant pathogens in New Zealand. Mycology 8(2): 59-66. http://dx.doi.org/10.1080/21501203.2016.1278409 (Journal Article, 2017)
  • Phillips RL, Song B, McMillan AMS, Grelet G, Weir BS, Palmada T, Tobias C 2016. Chemical formation of hybrid di-nitrogen calls fungal codenitrification into question. Scientific Reports 6: 39077. http://doi.org/10.1038/srep39077 (Journal Article, 2016)
  • Shivas RG, Tan YP, Edwards J, Dinh Q, Maxwell A, Andjic V, Liberato JR, Anderson C, Beasley DR, Bransgrove K, Coates LM, Cowan K, Daniel R, Dean JR, Lomavatu MF, Mercado-Escueta D, Mitchell RW, Thangavel R, Tran-Nguyen LTT, Weir BS 2016. Colletotrichum species in Australia. Australasian Plant Pathology 45(5): 447-464. http://doi.org/10.1007/s13313-016-0443-2 (Journal Article, 2016)
  • Réblová M, Miller AN, Rossman AY, Seifert KA, Crous PW, Hawksworth DL, Abdel-Wahab MA, Cannon PF, Daranagama DA, De Beer ZW, Huang S-K, Hyde KD, Jayawardena R, Jaklitsch W, Jones EBG, Ju Y-M, Judith C, Maharachchikumbura SSN, Pang K-L, Petrini LE, Raja HA, Romero AI, Shearer C, Senanayake IC, Voglmayr H, Weir BS, Wijayawarden NN 2016. Recommendations for competing sexual-asexually typified generic names in Sordariomycetes (except Diaporthales, Hypocreales, and Magnaporthales) IMA Fungus 7(1): 131-153. http://doi.org/10.5598/imafungus.2016.07.01.08 (Journal Article, 2016)
  • Callaghan SE, Puno VI, Williams AP, Weir BS, Balmas V, Sengsoulichan K, Phantavong S, Keovorlajak T, Phitsanoukane P, Xomphouthilath P, Phapmixay KS, Vilavong S, Liew ECY, Duckitt GS, Burgess LW 2016. First report of Fusarium oxysporum f.sp. niveum in the Lao PDR. Australasian Plant Disease Notes 11: 9. http://doi.org/10.1007/s13314-016-0191-8 (Journal Article, 2016)
  • Macedo DM, Pereira OL, Hora Júnior BT, Weir BS, Barreto RW 2016. Mycobiota of the weed Tradescantia fluminensis in its native range in Brazil with particular reference to classical biological control. Australasian Plant Pathology 45(1): 45-56. http://doi.org/10.1007/s13313-015-0388-x (Journal Article, 2016)
  • Thakur S, Weir BS, Guttman D 2016. Phytopathogen genome announcement: draft genome sequences of 62 Pseudomonas syringae type and pathotype strains. Molecular Plant-Microbe Interactions 29(4): 243-246. http://doi.org/10.1094/MPMI-01-16-0013-TA (Journal Article, 2016)
  • Phillips R, Grelet G, McMillan A, Song B, Weir B, Palmada T, Tobias C 2016. Fungal denitrification: Bipolaris sorokiniana exclusively denitrifies inorganic nitrogen in the presence and absence of oxygen. FEMS Microbiology Letters 363(4): fnw007. http://doi.org/10.1093/femsle/fnw007 (Journal Article, 2016)
  • Lopes-Santos L, Castro DBA, Ottoboni LMM, Park D, Weir BS, Destéfano SAL 2015. Draft genome sequence of Burkholderia andropogonis type strain ICMP2807, isolated from Sorghum bicolor. Genome Announcements 3(3): e00455-15. http://doi.org/10.1128/genomeA.00455-15 (Journal Article, 2015)
  • Weir BS, Paderes EP, Ananth N, Uchida JY, Pennycook SR, Bellgard SE, Beever RE 2015. A taxonomic revision of Phytophthora Clade 5 including two new species, Phytophthora agathidicida and P. cocois. Phytotaxa 205(1): 21-38. http://doi.org/10.11646/phytotaxa.205.1.2 (Journal Article, 2015)
  • Liu F, Weir BS, Damm U, Crous PW, Wang Y, Liu B, Wang M, Zhang M, Cai L 2015. Unravelling Colletotrichum species associated with Camellia: employing ApMat and GS loci to resolve species in the C. gloeosporioides complex. Persoonia 35: 63-86. http://dx.doi.org/10.3767/003158515X687597 (Journal Article, 2015)
  • Ireland KB, Weir BS, Phantavong S, Phitsanoukane P, Vongvichid K, Vilavong S, Tesoriero LA, Burgess LW 2014. First report of Rhizoctonia solani anastomosis group AG-4 HG-I in the Lao PDR. Australasian Plant Disease Notes 10: 1. http://dx.doi.org/10.1007/s13314-014-0152-z (Journal Article, 2014)
  • Taylor RK, Chapman JR, Romberg MK, Weir BS, Vanneste J, Everett R, Ward LI, Liefting LW, Lebas BSM, Alexander BJR 2014. Diagnostic challenges for the detection of emerging pathogens: a case study involving the incursion of Pseudomonas syringae pv. actinidiae in New Zealand. In: Gullino ML, Bonants PJM ed. Detection and diagnostics of plant pathogens. Plant Pathology in the 21st Century. 5. Dordrecht, Springer Netherlands. Pp. 71-86. http://dx.doi.org/10.1007/978-94-017-9020-8_5 (Book Section, 2014)
  • Weir B 2014. How to get good fungal and bacterial identifications from GenBank sequences. NZ Rhizobia. http://www.rhizobia.co.nz/ids-using-genbank updated 29 October 2014. (Web Page, 2014)
  • Schoch CL, Robbertse B, Robert V, Vu D, Cardinali G, Irinyi L, Meyer W, Nilsson RH, Hughes KJD, Miller AN, Kirk PM, Abarenkov K, Aime MC, Ariyawansa HA, Bidartondo M, Boekhout T, Buyck B, Cai Q, Chen J, Crespo A, Crous PW, Damm U, De Beer ZW, Dentinger BTM, Divakar PK, Dueñas M, Feau N, Fliegerova K, García MA, Ge Z-W, Griffith GW, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Gueidan C, Guo L, Hambleton S, Hamelin R, Hansen K, Hofstetter V, Hong S-B, Houbraken J, Hyde KD, Inderbitzin P, Johnston PR, Karunarathna SC, Kõljalg U, Kovács GM, Kraichak E, Krizsan K, Kurtzman CP, Larsson K-H, Leavitt S, Letcher PM, Liimatainen K, Liu J-K, Lodge DJ, Luangsa-ard JJ, Lumbsch HT, Maharachchikumbura SSN, Manamgoda D, Martín MP, Minnis AM, Moncalvo J-M, Mulè G, Nakasone KK, Niskanen T, Olariaga I, Papp T, Petkovits T, Pino-Bodas R, Powell MJ, Raja HA, Redecker D, Sarmiento-Ramirez JM, Seifert KA, Shrestha B, Stenroos S, Stielow B, Suh S-O, Tanaka K, Tedersoo L, Telleria MT, Udayanga D, Untereiner WA, Uribeondo JD, Subbarao KV, Vágvölgyi C, Visagie C, Voigt K, Walker DM, Weir BS, Weiß M, Wijayawardene NN, Wingfield MJ, Xu JP, Yang ZL, Zhang N, Zhuang W-Y, Federhen S 2014. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database 2014: bau061. http://dx.doi.org/10.1093/database/bau061 (Journal Article, 2014)
  • Dhami MK, Weir BS, Taylor MW, Beggs JR 2013. Diverse honeydew-consuming fungal communities associated with scale insects. PLoS ONE 8(7): e70316. http://dx.doi.org/10.1371/journal.pone.0070316 (Journal Article, 2013)
  • Cannon PF, Damm U, Johnston PR, Weir BS 2012. Colletotrichum - current status and future directions. Studies in mycology 73(1): 181-213. (Journal Article, 2012)
  • Weir BS, Johnston PR, Damm U 2012. The Colletotrichum gloeosporioides species complex. Studies in mycology 73(1): 115-80. (Journal Article, 2012)
  • Tan HW, Weir BS, Carter N, Heenan PB, Ridgway HJ, James EK, Sprent JI, Young JPW, Andrews M 2012. 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 7(10): e47677. http://dx.doi.org/10.1371/journal.pone.0047677 (Journal Article, 2012)
  • Padamsee MB, S., Dickie I, Fraser S, Park D, Stevenson B, Weir B 2012. [Poster abstract] Stuff in Duff: a metagenomic study of fungi in kauri forests. Proceedings: 80th Meeting of the Mycological Society of America, Yale University, New Haven, CT, 15-18 July 2012. http://msafungi.org/wp-content/uploads/Inoculum/63%283%29.pdf (Conference Proceedings, 2012)
  • Chapman JR, Taylor RK, Weir BS, Romberg MK, Vanneste JL, Luck J, Alexander BJR 2012. Phylogenetic relationships among global populations of Pseudomonas syringae pv. actinidiae. Phytopathology 102(11): 1034-1044. http://dx.doi.org/10.1094/PHYTO-03-12-0064-R (Journal Article, 2012)
  • Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Weir BS, Johnston PR, Park D, Consortium FB 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109(16): 6241-6246. <Go to ISI>://WOS:000303246100068 (Journal Article, 2012)
  • Damm U, Cannon PF, Woudenberg JHC, Johnston PR, Weir BS, Tan YP, Shivas RG, Crous PW 2012. The Colletotrichum boninense species complex. Studies in mycology 73: 1-36. http://www.studiesinmycology.org/content/early/2012/02/29/sim0002.full.pdf+html (Journal Article, 2012)
  • Hawksworth DL, Crous PW, Redhead SA, Reynolds DR, Samson R, Seifert KA, Taylor JW, Wingfield MJ, Johnston P, Pennycook SR, Weir B, al. e 2011. The Amsterdam declaration on fungal nomenclature. IMA fungus 2(1): 105-112. http://www.ingentaconnect.com/content/ima/imafung/pre-prints/s14 (Journal Article, 2011)
  • Weir BS, Johnston PR 2010. Characterisation and neotypification of Gloeosporium kaki Hori as Colletotrichum horii nom. nov. Mycotaxon 111: 209-219. (Journal Article, 2010)
  • Cai L, Hyde KD, Taylor PWJ, Weir BS, Waller JM, Abang MM, Zhang JZ, Yang YL, Phoulivong S, Liu ZY, Prihastuti H, Shivas RG, McKenzie EHC, Johnston PR 2009. A polyphasic approach for studying Colletotrichum. Fungal diversity 39: 185-206. (Journal Article, 2009)
  • Hyde KD, Cai L, Cannon PF, Crouch JA, Crous PW, Damm U, Goodwin PH, Chen H, Johnston PR, Jones EBG, Liu ZY, McKenzie EHC, Moriwaki J, Noireung P, Pennycook SR, Pfenning LH, Prihastuti H, Sato T, Shivas RG, Tan YP, Taylor PWJ, Weir BS, Yang YL, Zhang JZ 2009. Colletotrichum - names in current use. Fungal diversity 39: 147-183. (Journal Article, 2009)
  • Graham AB, Johnston PR, Weir BS 2009. Three new Phaeoacremonium species on grapevines in New Zealand. Australasian plant pathology 38(5): 505-513. (Journal Article, 2009)
  • Liefting LW, Sutherland PW, Ward LI, Paice KL, Weir BS, Clover GRG 2009. A new 'Candidatus Liberibacter' species associated with diseases of solanaceous crops. Plant disease 93(3): 208-214. (Journal Article, 2009)
  • Liefting LW, Weir BS, Pennycook SR, Clover GRG 2009. 'Candidatus Liberibacter solanacearum', associated with plants in the family Solanaceae. International journal of systematic and evolutionary microbiology 59(9): 2274-2276. (Journal Article, 2009)

Memberships

Memberships

  • Leadership Group, EcoGene®
  • Professional Member, Royal Society New Zealand
  • Curator, ICMP culture collection
  • Treasurer and Webmaster, Fungal Network of New Zealand (FUNNZ)
  • Secretary, International Sub commission on Colletotrichum Taxonomy (ISTC)
  • Councillor, Australasian Mycological Society
  • Deputy Theme Leader, Theme 3 - Diagnostics, B3

Skills

Skills

  • Bacteriology
  • Microbiology
  • Phylogenetics
  • Molecular Biology
  • Molecular Systematics
  • Plant Pathology
  • Mycology
  • Biosystematics
  • Mushrooms