Bevan Simon Weir

• PhD
• Research Leader, ICMP Curator at Manaaki Whenua - Landcare Research

Isolates of a variety of fungal plant pathogens (Alternaria radicina ICMP 5619, Cercospora beticola ICMP 15907, Dactylonectria macrodidyma ICMP 16789, D. torresensis ICMP 20542, Ilyonectria europaea ICMP 16794, and I. liriodendra ICMP 16795) were screened for antimicrobial activity against the human pathogenic bacteria Acinetobacter baumannii, Pseu...

Kākāpō are a critically endangered parrot restricted to a few islands off the coast of New Zealand. Kākāpō are very closely monitored, especially during nesting seasons. In 2019, during a highly successful nesting season, an outbreak of aspergillosis affected 21 individuals and led to the deaths of 9, leaving a population of only 211 kākāpō. In mon...

Antimicrobial compounds, including antibiotics, have been a cornerstone of modern medicine being able to both treat infections and prevent infections in at-risk people, including those who are immune-compromised and those undergoing routine surgical procedures. Their intense use, including in people, animals, and plants, has led to an increase in t...

Background: The critically endangered kākāpō is a flightless, nocturnal parrot endemic to Aotearoa New Zealand. Recent efforts to describe the gastrointestinal microbial community of this threatened herbivore revealed a low-diversity microbiota that is often dominated by Escherichia-Shigella bacteria. Given the importance of associated microbial c...

Biological collections preserve our past, while helping protect our future and increase future knowledge. Plant bacterial culture collections are our security for domestic and global biosecurity. This feature article will provide an introduction to the global position of plant bacterial collections. The role of collections in monitoring plant patho...

Screening of several fungi from the New Zealand International Collection of Microorganisms from Plants identified two strains of Penicillium, P. bissettii and P. glabrum, which exhibited antimicrobial activity against Escherichia coli,Klebsiella pneumoniae, and Staphylococcus aureus. Further investigation into the natural products of the fungi, thr...

There is a real and urgent need for new antibiotics able to kill Mycobacteria, acid-fast bacilli capable of causing multiple deadly diseases. These include members of the Mycobacterium tuberculosis complex, which causes the lung disease tuberculosis (TB) as well as non-tuberculous Mycobacteria (NTM) a growing cause of lung, skin, soft tissue, and o...

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distin...

Fungi have become an invaluable source of bioactive natural products, with more than 5 million species of fungi spanning the globe. Fractionation of crude extract of Neodidymelliopsis sp., led to the isolation of a novel polyketide, (2Z)-cillifuranone (1) and five previously reported natural products, (2E)-cillifuranone (2), taiwapyrone (3), xylari...

Slow growing oomycete isolates with morphological resemblance to Phytophthora were obtained from forest streams during routine monitoring for the EU quarantine forest pathogen Phytophthora ramorum in Ireland and Northern Ireland. Internal Transcribed Spacer (ITS) sequence analysis indicated that they belonged to two previously unknown species of No...

Antimicrobial bioassay-guided fractionation of the endophytic fungi Neofusicoccum australe led to the isolation of a new unsymmetrical naphthoquinone dimer, neofusnaphthoquinone B (1), along with four known natural products (2–5). Structure elucidation was conducted by nuclear magnetic resonance (NMR) spectroscopic methods, and the antimicrobial ac...

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 p...

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 p...

Antimicrobial bioassay-guided fractionation of Microcera larvarum led to the isolation of a γ-lactone with a furo[3,4-b]pyran-5-one bicyclic ring system (1) and three known compounds, (3S,4R)-4-hydroxymellein (2), (3S,4S)-4-hydroxymellein (3) and 7-hydroxy-3-(1-hydroxyethyl)isobenzofuran-1(3H)-one (4). Structure elucidation was conducted by NMR spe...

Coniella hibisci is reported for the first time in Lao P.D.R. The pathogen was isolated from roselle (Hibiscus sabdariffa var. sabdariffa) stem and leaf samples from a farm in Thateng district, Sekong province, and deposited with the International Collection of Microorganisms from Plants (ICMP). The identification of the pathogen was based on morph...

Kauri (Agathis australis), which is one of the world's largest and longest‐living conifer species, is under threat from a root and collar dieback disease caused by the oomycete pathogen Phytophthora agathidicida. The noted incidence of kauri dieback has increased in the past decade, and even trees >1000 years old are not immune. This disease has pr...

Diverse Gram-negative pathogens like Pseudomonas syringae 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. Consequen...

Hexaploid Caucasian clover was grown in soil sampled at three New Zealand South Island high country sites to which specific rhizobium inoculum had been added with sowing of the legume in 1975, 1992 and 1997; two sites on the Lincoln University farm sown with inoculated Caucasian clover in 2012 and 2013; and six sites not sown with the crop. Caucasi...

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...

Diverse Gram-negative pathogens like Pseudomonas syringae 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 towards plant immunity. Conseque...

Our recent project supported through Unlocking Curious Minds funding from New Zealand’s Ministry of Business Innovation and Employment enabled us to introduce school students to the fascinating, yet frequently forgotten, fungal kingdom. In this project, we demystified the science of species discovery. We collaborated with students at three schools...

This corrects the article DOI: 10.1038/srep39077.

Novel species of fungi described in this study include those from various countries as follows: Australia: Banksiophoma australiensis (incl. Banksiophoma gen. nov.) on Banksia coccinea, Davidiellomyces australiensis (incl. Davidiellomyces gen. nov.) on Cyperaceae, Didymocyrtis banksiae on Banksia sessilis var. cygnorum, Disculoides calophyllae on C...

Epicoccum nigrum 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.

The phylogenetic classification of the species Burkholderia andropogonis within the Burkholderia genus was reassessed using 16S rRNA gene phylogenetic analysis and multilocus sequence analysis (MLSA). Both phylogenetic trees revealed two main groups, named A and B, strongly supported by high bootstrap values (100%). Group A encompassed all of the B...

Dacrymycetes, sister to Agaricomycetes, is a noteworthy lineage for studying the evolution of wooddecaying basidiomycetes; however, its species diversity and phylogeny are largely unknown. Species of Dacrymycetes previously used in molecular phylogenetic analyses are mainly derived from the Northern Hemisphere, thus insufficient knowledge exists co...

The Landcare Research collections of biological specimens and their associated databases provide an essential resource for local and international researchers, administrators of New Zealand’s plant-disease-related biosecurity system, border control agencies and non-professional citizen scientists. This article focuses on data provided for New Zeala...

Removal of excess nitrogen (N) can best be achieved through denitrification processes that transform N in water and terrestrial ecosystems to di-nitrogen (N2) gas. The greenhouse gas nitrous oxide (N2O) is considered an intermediate or end-product in denitrification pathways. Both abiotic and biotic denitrification processes use a single N source t...

Forty-four species of Colletotrichum are confirmed as present in Australia based on DNA sequencing analyses. Many of these species were identified directly as a result of two workshops organised by the Subcommittee on Plant Health Diagnostics in Australia in 2015 that covered morphological and molecular approaches to identification of Colletotrichu...

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...

Fusarium oxysporum f.sp. niveum is reported for the first time in the Lao PDR. It was isolated from watermelons (Citrullus lanatus) in Songkhon district, Savannahkhet province following a limited ad hoc survey during January and February of 2015. Infected plants showed symptoms of wilt, vascular discolouration, necrosis in the collar region, lower...

Ralstonia pseudosolanacearum is reported for the first time from the Lao PDR. Typical symptoms of wilt and vascular exudate were observed in potatoes and tomatoes in Paksong district, Champasak province. Pathogenicity was proven and identification was based on symptoms, commercial diagnostic test kits and sequence of the egl gene.

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.

We investigated the phylogenetic diversity of 144 Colletotrichum isolates associated with symptomatic and asymptomatic tissues of Camellia sinensis and other Camellia spp. from seven provinces in China (Fujian, Guizhou, Henan, Jiangxi, Sichuan, Yunnan, Zhejiang), and seven isolates obtained from other countries, including Indonesia, UK, and the USA...

Tradescantia fluminensis [Commelinaceae] (common name wandering Jew or trad), is a native Brazilian herbaceous plant, which has been introduced to be used as an ornamental in many warm areas of the world. In New Zealand and other countries it has become an aggressive invader of natural ecosystems, causing serious environmental disturbances and thre...

Fungi may play an important role in the production of the greenhouse gas nitrous oxide (N2O). Bipolaris sorokiniana is a ubiquitous saprobe found in soils worldwide, yet denitrification by this fungal strain has not previously been reported. We aimed to test if B. sorokiniana would produce N2O and CO2 in the presence of organic and inorganic forms...

Phytophthora Clade 5 is a very poorly studied group of species of oomycete chromists, consisting of only two known species P. castaneae (≡ P. katsurae, nom. illegit.) and P. heveae with most isolates from East Asia and the Pacific Islands. However, isolates of two important disease-causing chromists in Clade 5, one of kauri (Agathis australis) in N...

Here, we report the draft genome sequence of Burkholderia andropogonis ICMP2807, a phytopathogenic bacterium isolated from Sorghum bicolor plants in the United States. FOOTNOTES Address correspondence to Suzete Aparecida Lanza Destéfanoa, suzete{at}biologico.sp.gov.br. Citation Lopes-Santos L, Castro DBA, Ottoboni LMM, Park D, Weir BS, Destéfano SA...

Phytophthora Clade 5 is a very poorly studied group of species of oomycete chromists, consisting of only two known species P. castaneae (≡ P. katsurae, nom. illegit.) and P. heveae with most isolates from East Asia and the Pacific Islands. However, isolates of two important disease-causing chromists in Clade 5, one of kauri (Agathis australis) in N...

Rhizoctonia solani anastomosis group AG-4 HG-I is reported for the first time from the Lao PDR. It was isolated from gai lan (Brassica oleracea var. alboglabra) affected by collar rot, seedling death, root rot and stunting of older plants from the Paksong area of Champasak province. The anastomosis group was confirmed by sequencing and Koch’s postu...

In November 2010, Pseudomonas syringae pv. actinidiae (Psa) was detected for the first time in New Zealand. This finding triggered one of the largest surveillance and diagnostic programmes seen in New Zealand’s horticultural industry. During this response, over 912 kiwifruit orchards and 14,500 samples were screened and tested for the presence of P...

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 us...

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-pyrosequenci...

Diversity indices for the sooty mould community diversity observed from all samples in the ITS-t-RFLP dataset. H = Shannon index, simp = simpson index, invsimp = inverse simpson index, unbias.simp = unbiased simpson index and alpha = α coefficient of Fisher log series. (TIF)

List of ITS-based pyrosequencing samples and their respective FLX specific fusion tag-primers and their sequences. (DOCX)

Site influence on the composition of sooty mould community associated with Ultracoelostoma brittini honeydew. Plot A shows the multidimensional scaling plot based on T-RFLP peak-profiles using Bray-Curtis distances with grey squares = Mt Richardson (n = 9) and black circles = Lake Rotoiti (hosts pooled, n = 10); Plot B shows the principle coordinat...

Site influence on the sooty mould community composition using different molecular and analysis methods. Samples of sooty mould associated with Ultracoelostoma brittini from Lake Rotoiti and Mt Richardson were compared. (DOCX)

Rarefaction curves showing the alpha diversity estimates Phylogenetic Diversity (PD) (top) and chao 1 (bottom). Multiple rarefactions were performed using the method built in the QIIME pipeline. Briefly, OTU tables were rarefied with a minimum of 10 sequences/sample up to a maximum of 4000 sequences/sample, with stepsize = 10 sequences/sample and 1...

Anthracnose disease caused by the Colletotrichum gloeosporioides species complex is a major problem worldwide. In this study, we investigated the phylogenetic diversity of 207 Indian Colletotrichum isolates, associated with symptomatic and asymptomatic tissues of mango, belonging to this species complex. Phylogenetic analyses were performed based o...

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 Carmichaelina...

Unlabelled: Although only recently described, Colletotrichum boninense is well established in literature as an anthracnose pathogen or endophyte of a diverse range of host plants worldwide. It is especially prominent on members of Amaryllidaceae, Orchidaceae, Proteaceae and Solanaceae. Reports from literature and preliminary studies using ITS sequ...

The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within the Colletotrichum ITS gene tree. All taxa accepted within this clade are morphologically more or less typical of the broadly defined C. gloeosporioides, as it has been applied in the literature for the past 50 years. W...

A review is provided of the current state of understanding of Colletotrichum systematics, focusing on species-level data and the major clades. The taxonomic placement of the genus is discussed, and the evolution of our approach to species concepts and anamorph-teleomorph relationships is described. The application of multilocus technologies to phyl...

A species concept for Phytophthora "taxon Agathis" – causal agent of kauri dieback in New Zealand 1 • Phytophthora "taxon Agathis" (PTA) has been identifi ed (Beever et al. 2009) as a causal agent of kauri (Agathis australis) dieback in northern New Zealand (Figs 1 & 2). • Originally misidentifi ed as the morphologically similar P. heveae (Gadgil 1...

ABSTRACT Pseudomonas syringae pv. actinidiae, the causal agent of canker in kiwifruit (Actinidia spp.) vines, was first detected in Japan in 1984, followed by detections in Korea and Italy in the early 1990s. Isolates causing more severe disease symptoms have recently been detected in several countries with a wide global distribution, including Ita...

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes l...