Anne M Alvarez

University of Hawaiʻi at Mānoa | UH Manoa · Department of Plant and Environmental Protection Sciences

Irrigation water is a common source of contamination that carries plant and foodborne human pathogens and provides a niche for proliferation and survival of microbes in agricultural settings. Bacterial communities and their functions in irrigation water were investigated by analyzing samples from wetland taro farms on Oahu, Hawaii using different D...

Dickeya fangzhongdai, a bacterial pathogen of taro (Colocasia esculenta), onion (Allium sp.), and several species in the orchid family (Orchidaceae) causes soft rot and bleeding canker diseases. No field-deployable diagnostic tool is available for specific detection of this pathogen in different plant tissues. Therefore, we developed a field-deploy...

The Gram-positive genus Clavibacter is currently divided into seven species ( Clavibacter michiganensis , Clavibacter nebraskensis , Clavibacter capsici , Clavibacter sepedonicus , Clavibacter tessellarius , Clavibacter insidiosus and Clavibacter zhangzhiyongii ) and three subspecies ( C. michiganensis subsp. californiensis , C. michiganensis subsp...

Irrigation water is a potential source of contamination that carries plant and foodborne human pathogens and provides a niche for survival and proliferation of microbes in agricultural settings. This project investigated bacterial communities and their functions in the irrigation water from wetland taro farms on Oahu, Hawaii using different DNA seq...

Dickeya fangzhongdai , a bacterial pathogen of taro ( Colocasia esculenta ), onion ( Allium sp.), and several species in the orchid family ( Orchidaceae ), causing soft rot and bleeding canker diseases. No field-deployable diagnostic tool is available for specific detection of this pathogen in different plant tissues. Therefore, we developed a fiel...

Bacterial wilt strains in the Ralstonia solanacearum species complex (RSSC) pose serious threats to economically important crops worldwide. In 2014, Safni and co-workers proposed the reclassification of RSSC into three genomospecies: R. solanacearum (Rsol), R. pseudosolanacearum (Rpseu), and R. syzygii (Rsyz). The revision requires the proper ident...

Pectobacterium , agenus comprising gram-negative, pectinolytic phytopathogens, is responsible for economic losses in a wide host range of plants. In this study, the bacterial strains PL152 T and PL155 were isolated from taro corms in Hawai’i in 2018, and characterized using genomic and biochemical assays. The Next Generation Sequencing technologies...

The Gram-positive Clavibacter genus is currently divided into seven species ( C. michiganensis , C. nebraskensis , C. capsici , C. sepedonicus , C. tessellarius , C. insidiosus and C. zhangzhiyongii ) and three subspecies ( C. michiganensis subsp. californiensis , C. michiganensis subsp. chilensis and C. michiganensis subsp. phaseoli ). Recent stud...

Bacterial pathogens identified as Dickeya sp. have recently been associated with a corm rot of wetland taro on Oahu, Hawaii, but the species designation of these strains was unclear. A Gram-negative, pectinolytic bacterial strain PL65 isolated from an infected taro corm was subjected to polyphasic analysis to determine its genomic and phenotypic ch...

Aim The newly defined species P. parmentieri has emerged as an aggressive pathogen that causes soft rot and blackleg diseases on potato and has been widely disseminated across the globe, jeopardizing the productivity and potato food safety. The implementation of a fast and accurate detection tool is imperative to control, monitor and prevent furthe...

Dickeya zeae, a bacterial plant pathogen of the family Pectobacteriaceae, is responsible for a wide range of diseases on potato, maize, rice, banana, pineapple, taro, and ornamentals and significantly reduces crop production. D. zeae causes the soft rot of taro (Colocasia esculenta) and the heart rot of pineapple (Ananas comosus). In this study, we...

Clavibacter is an agriculturally important bacterial genus comprising nine host-specific species/subspecies including C. nebraskensis (Cn), which causes Goss's wilt and blight of maize. A robust, simple, and field-deployable method is required to specifically detect Cn in infected plants and distinguish it from other Clavibacter species for quarant...

Mizuna (Brassica rapa var. japonica), a member of family Brassicaceae, is a leafy vegetable having phenolic and other compounds beneficial to human health, such as natural antioxidants (Khanam et al. 2012). In October 2020, a field of mizuna (variety: Early) on Oahu island was observed having 20-30% diseased plants. Four randomly selected infected...

Dickeya zeae, a bacterial plant pathogen in the family Pectobacteriaceae, is responsible for a wide range of diseases on potato, maize, rice, banana, pineapple, taro and ornamentals and significantly reduces crop production; D. zeae causes soft rot of taro (Colocasia esculenta) and heart rot of pineapple (Ananas comosus). In this study, we used Pac...

Aim: Clavibacter michiganensis (Cm) is a seed-borne plant pathogen that significantly reduces tomato production worldwide. Due to repeated outbreaks and rapid spread of the disease, seeds/transplants need to be certified free of the pathogen before planting. To this end, we developed a multiplex TaqMan qPCR assay that can accurately detect Cm in i...

The bacterial wilt pathogen, first known as Bacillus solanacearum, has undergone numerous taxonomic changes since its first description in 1896. The history and significance of this pathogen is covered in this review with an emphasis on the advances in technology that were used to support each reclassification that finally led to the current separa...

The bacterial wilt pathogen, first known as Bacillus solanacearum, has undergone numerous taxonomic changes since its first description in 1896. The history and significance of this pathogen is covered in this review with an emphasis on the advances in technology that were used to support each reclassification that finally led to the current separa...

Clavibacter is an agriculturally important bacterial genus comprising nine host-specific species/subspecies including C. nebraskensis ( Cn ), which causes Goss’s wilt and blight of maize. A robust, simple, and field-deployable method is required to specifically detect Cn in infected plants and distinguish it from other Clavibacter species for quara...

Dickeya spp. cause blackleg and soft rot diseases of potato and several other plant species worldwide, resulting in high economic losses. Rapid detection and identification of the pathogen is essential for facilitating efficient disease management. Our aim in this research was to develop a rapid and field-deployable recombinase polymerase amplifica...

Aims: Dickeya species are high consequence plant pathogenic bacteria; associated with potato disease outbreaks and subsequent economic losses worldwide. Early, accurate, and reliable detection of Dickeya spp. is needed to prevent establishment and further dissemination of this pathogen. Therefore, a multiplex TaqMan qPCR was developed for sensitiv...

Aims Dickeya species are high consequence plant pathogenic bacteria listed among the quarantine pathogens of the European Union; associated with potato disease outbreaks and subsequent economic losses worldwide. Early, accurate, and reliable detection of Dickeya spp. is needed to prevent establishment and further dissemination of this pathogen. The...

Ironwood (Casuarina equisetifolia subsp. equisetifolia) trees on Guam have been in decline since 2002. This study applied proportional odds logistic multiple regression modeling to a set of biological variables in order to find significant decline predictors as a first step towards identifying pathogenic contributors. Based on the analysis of a set...

Bacterial leaf spot of tomato and pepper (BLS), an economically important bacterial disease caused by four species of Xanthomonas (X. euvesicatoria (Xe), X. vesicatoria (Xv), X. gardneri (Xg), and X. perforans (Xp)), is a global problem and can cause over 50% crop loss under unfavorable conditions. Among the four species, Xe and Xv are prevalent wo...

Clavibacter is an agriculturally important genus comprising a single species, Clavibacter michiganensis, and multiple subspecies, including, C. michiganensis subsp. nebraskensis which causes Goss's wilt/blight of corn, accounts for high yield losses and is listed among the five most significant diseases of corn in the United States of America. Our...

Clavibacter is an agriculturally important genus comprising a single species, Clavibacter michiganensis, and multiple subspecies, including, C. michiganensis subsp. nebraskensis which causes Goss's wilt/blight of corn and accounts for high yield losses - listed among the five most significant diseases of corn in the United States of America. Our re...

Pectobacterium species cause serious bacterial soft rot diseases worldwide on economically important fruit and vegetable crops including tomato and potato. Accurate and simple methods are essential for rapid pathogen identification and timely management of the diseases. Recombinase polymerase amplification (RPA) combined with a lateral flow device...

Aims Clavibacter michiganensis is an important bacterial plant pathogen that causes vast destruction to agriculturally important crops worldwide. Early detection is critical to evaluate disease progression and to implement efficient control measures to avoid serious epidemics. In this study, we developed a sensitive, specific and robust loop‐mediat...

Bacterial spot (BS), caused by Xanthomonas euvesicatoria, X. vesicatoria, X. gardneri and X. perforans, is an economically important bacterial disease of tomato and pepper. Symptoms produced by all four species are nearly indistinguishable. At present, no point-of-care diagnostics exist for BS. In this research, we examined genomes of X. euvesicato...

Soft rot caused by Pectobacterium carotovorum is one of most common bacterial diseases occurring in fruits and vegetables worldwide, yet consumer-acceptable options for post-harvest disease management are still insufficient. We evaluated the effect of potassium tetraborate tetrahydrate (B 4 K 2 O 7 .4H 2 O) (PTB) on the growth of P. carotovorum usi...

Dickeya and Pectobacterium spp. are responsible for soft rotting diseases of several plant species, some with overlapping host range. On potato, symptoms caused by these pathogens cannot be clearly differentiated. Disease results in the down-grading and rejection of potato seed, thus requiring additional phytosanitary restrictions across Northern E...

Gray mold and soft rot are the most important postharvest diseases of tomato worldwide. A survey of fresh-market tomato fruit was conducted in Oahu to determine which fungal and bacterial pathogens were most commonly associated with postharvest disease. Alternaria, Botrytis, Colletotrichum, Fusarium, Geotrichum, Mucor, Stemphyllium, Rhizopus and Pe...

The United States Culture Collection Network was formed in 2012 by a group of culture collection scientists and stakeholders in order to continue the progress established previously through efforts of an ad hoc group. The network is supported by a Research Coordination Network grant from the US National Science Foundation (NSF) and has the goals of...

Potatoes are an important agroeconomic crop worldwide and maceration diseases caused by pectolytic bacterial pathogens result in significant pre- and postharvest losses. Pectobacterium carotovorum shares a common host range with other Pectobacterium spp. and other members of the Enterobacteriaceae such as Dickeya spp. As these pathogens cannot be c...

The Goss's wilt pathogen, Clavibacter michiganensis subsp. nebraskensis, can cause considerable losses in maize (Zea mays L.) production. Diagnosis of Goss's wilt currently is based on symptomology and identification of C. michiganensis subsp. nebraskensis, following isolation on a semi-selective medium and/or serological testing. In an effort to p...

A loop-mediated amplification (LAMP) assay developed previously to specifically identify Clavibacter michiganensis subsp. michiganensis, the causal agent of bacterial canker of tomato, was compared with a commercial lateral flow immunoassay, three PCR assays, and culturing on agar medium for efficacy in detecting the pathogen in pepper and tomato t...

Clavibacter michiganensis subsp. michiganensis (Cmm) is an important seedborne pathogen that causes bacterial canker of tomato and significant crop losses worldwide. Few studies document the long-term survival of Cmm in infected seed and less is known about the relationship between inoculum levels and resulting plant infection. Greenhouse studies w...

The genus Clavibacter contains one recognized species, Clavibacter michiganensis. Clavibacter michiganensis is subdivided into subspecies based on host specificity and bacteriological characteristics, with Clavibacter michiganensis subspecies michiganensis (Cmm) causing bacterial canker of tomato. Cmm is often spread through contaminated seed leadi...

Bacterial canker of tomato, caused by Clavibacter michiganensis subsp. michiganensis (Cmm), occurs worldwide. This study focuses on three genes, clvA (clavicidin) and two associated genes (clvF and clvG, encoding a putative ABC-type multidrug transport system ATPase and permease component, respectively). Loop-mediated amplification of clvA and PCR...

Bacterial heart rot caused by a yet undetermined species of Dickeya was first observed in December 2003 in Oahu, HI, on a pineapple cultivar (Ananas comosus 'PRI 73-114') recently imported from Central America. Identical symptoms were later seen in the same plantation in fields that had been planted with propagules from the Philippines. Dickeya str...

Ironwood (Casuarina equisetifolia subsp. equisetifolia) is a nitrogen-fixing tree of considerable social, economic and environmental importance that commonly occurs in tropical/subtropical zones of Asia, the Pacific, Africa, and Central America. Ironwood decline was first noticed on Guam in 2002 and is now affecting thousands of trees and impacting...

Bacterial heart rot of pineapple reported in Hawaii in 2003 and reoccurring in 2006 was caused by an undetermined species of Dickeya. Classification of the bacterial strains isolated from infected pineapple to one of the recognized Dickeya species and their phylogenetic relationships with Dickeya were determined by a multilocus sequence analysis (M...

Bacterial black spot of mango (Mangifera indica) caused by Xanthomonas citri pv. mangiferaeindicae (Xcm), is an economically important disease in tropical and subtropical areas (3). Xcm can infect a wide range of mango cultivars and induces raised, angular, black leaf lesions, sometimes with a chlorotic halo. Fruit symptoms appear as small, water-s...

Loop-mediated amplification (LAMP) was used to specifically identify Clavibacter michiganensis subsp. michiganensis (Cmm), causal agent of bacterial canker of tomato. LAMP primers were developed to detect micA, a chromosomally stable gene that encodes a type II lantibiotic, michiganin A, which inhibits growth of other C. michiganensis subspecies. F...

The goal of successful diagnostic test development is to identify specific markers that give positive reactions with all target strains and negative reactions with non-target contaminants. However, this goal is rarely achieved with complete satisfaction. Therefore, a rational compromise between sensitivity and specificity, based on a better underst...

We used micro- and resonance Raman spectroscopy with 785 nm and 514.5 nm laser excitation, respectively, to characterize a plant pathogenic bacteria, Xanthomonas axonopodis pv. dieffenbachiae D150. The bacterial genus Xathomonas is closely related to bacterial genus Stenotrophomonas that causes an infection in humans. This study has identified for...

Essential oils of palmarosa, lemongrass, and eucalyptus have shown promise as biofumigants for control of the bacterial wilt disease of edible ginger (Zingiber officinale) caused by Ralstonia solanacearum race 4 in previous potting medium studies. Biochemical changes in R. solanacearum cells were evaluated with micro-Raman spectroscopy following tr...

New rapid diagnostic methods are urgently needed to discriminate the quarantine pathogen Ralstonia solanacearum (Rs) race 3 biovar 2 (R3B2) from other populations of Rs that lack the adaptation to cause bacterial wilt disease in temperate regions. We used an in silico bioinformatic approach to identify several genome sequences potentially specific...

Average between group distances of the RIF marker from ten different Pectobacterium RIF sequences. (PDF)

Average between group distances of the RIF marker from ten different Dickeya RIF sequences. (PDF)

In silico comparison of Xanthomonas with the RIF marker resolves one pair of closely related strains that is unresolved with four other housekeeping genes and the ITS. (PDF)

Multiple sequence alignment of nucleotides 311 to 1311 of the dnaA genes of six genera. Primer regions are shown for Clavibacter, Xanthomonas, Ralstonia, Erwinia, Dickeya and Pectobacterium. Primer binding regions are shown in red with black background. The AAA+ domain (green) [52] and the C-terminal domain (pink) [52] are highlighted. (TIF)

RIF distinguishes more Xanthomonas strains than ITS. Unrooted neighbor-joining trees for the RIF and ITS markers were constructed from eighty-four Xanthomonas strains from the PBC (Supplemental Table S2) and eight reference strains from GenBank (see Table 1 for strain names) . Identical sequences are represented only once and the number of sequence...

RIF sequences distinguish fewer strains of Clavibacter but produce a more robust tree. Unrooted neighbor-joining trees for the RIF and ITS markers were constructed from nineteen Clavibacter strains from the PBC (Supplemental Table S2) and two reference strains from GenBank (see Table 1 for strain names). Identical sequences are represented only onc...

RIF sequences distinguish more Dickeya strains than ITS. Unrooted neighbor-joining trees for the RIF and ITS markers were constructed from twenty-nine Dickeya strains from the PBC (Supplemental Table S2) and three reference strains (with strain names) from GenBank (Supplemental Table S1). Identical sequences are represented only once and the number...

Strains used in this study. (PDF)

Computational derivation of a universal DNA marker from fifteen completely sequenced genomes was unsuccessful. (DOC)

RIF sequences distinguish more Ralstonia strains than ITS. Unrooted neighbor-joining trees for the RIF and ITS markers were constructed from ninety-seven Ralstonia strains from the PBC (Supplemental Table S2) and three reference strains from GenBank (see Table 1 for strain names). Identical sequences are represented only once and the number of sequ...

X. albilineans is more distantly related to other Xanthomonas species than is Stenotrophomonas maltophilia . (PDF)

Copy number and location of the dnaA genes in 1,067 sequenced NCBI strains. (PDF)

Average between species distances of the RIF marker from twenty-three different Ralstonia RIF sequences. (PDF)

Average between subspecies distances of the RIF sequence from eleven different Clavibacter michiganensis RIF sequences. (PDF)

A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the rRNA genes, dnaA is a single copy gene in the vas...