Erwinia billingiae causes bacterial Canker of Mango (Mangifera indica) in Costa Rica

Introduction. In Costa Rica, bacterial canker of mango has caused economic losses in most of the productive areas since the mid-1980s. The causal agents have been identified only by phenotypic methods such as Erwinia mangifera and E. herbicola. Objective. To confirm, using a molecular and phenotypic approach, the species of the Enterobacteriaceae the cause bacterial canker of mango in Costa Rica. Material and methods. Fruits, branches, and trunks with symptoms were collected in different orchards in the Alajuela province. Bacterial isolation was performed, and pathogenicity was evaluated by inoculating fruits and trunks of the Tommy Atkins variety. The positive isolates for the pathogenic test were re-inoculated, isolated, and identified in order to fulfill Koch’s postulates. The CIBCM-Mg-115 positive isolate that caused symptoms was analyzed by complete biochemical characterization and molecular identification by phylogenetic analyses of 16S rRNA and the atpD, gyrB, infB, and rpoB housekeeping genes. Results. According to the data obtained from the biochemical and molecular analysis, the CIBCM-Mg-115 strain was identified as Erwinia billingiae. Conclusion. E. billingiae corresponds to one of the causal agents of bacterial canker on mango (M. indica) trees in Costa Rica.

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Bacterial Canker Disease on Populus × euramericana Caused by Lonsdalea populi in Serbia

Forests ◽

10.3390/f11101080 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1080

Author(s):

Milica Zlatković ◽

Imola Tenorio-Baigorria ◽

Tamás Lakatos ◽

Tímea Tóth ◽

András Koltay ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Test Chamber ◽

Housekeeping Genes ◽

Rrna Gene ◽

Bacterial Disease ◽

Bacterial Canker ◽

Canker Disease ◽

Populus Euramericana ◽

First Report ◽

Eastern Cottonwood

Populus × euramericana (Dode) Guinier clone (cl.) “I-214” is a fast-growing interspecific hybrid between Eastern cottonwood (P. deltoides Bartr. ex Marsh) and European black poplar (Populus nigra L.). Populus × euramericana was introduced into Serbia in the 1950s and has become one of the most widely grown poplar species. In September 2019, cankers were observed on stems and branches of P. × euramericana cl. “I-214” trees in a two-year-old poplar plantation in the province of Vojvodina, Serbia. The canker tissue was soft and watery, and a colorless fluid that smelled rotten flowed from the cracks in the bark, suggesting possible bacterial disease. After two weeks, diseased trees experienced crown die-back and oozing of foamy, odorous exudates and this study aimed to identify the causal agent of the disease. Canker margins and exudates were collected from 20 symptomatic trees. The associated bacterium was isolated and identified using biochemical characteristics, phylogenetic analyses based on 16S rRNA gene sequences, and multilocus sequence analyses (MLSA) based on partial sequencing of three housekeeping genes (gyrB, infB, and atpD). The pathogen was identified as Lonsdalea populi. Pathogenicity tests were conducted on rooted cuttings of P. × euramericana cl. “I-214” in an environmental test chamber and demonstrated that the isolated bacterial strain was able to reproduce symptoms of softened, water-soaked cankers and exudation. To the best of our knowledge, this is the first report of L. populi causing bacterial canker disease on P. × euramericana cl. “I-214” in Serbia and in southeastern Europe (SEE). It is also the first report of a bacterial disease on hybrid poplars, including P. × euramericana in this country and in SEE. If the disease spreads into new areas, selection for L. populi resistance may need to be integrated into future poplar breeding programs.

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Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin

ISME Communications ◽

10.1038/s43705-021-00027-x ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Rui Zhao ◽

Jennifer F. Biddle

Keyword(s):

Costa Rica ◽

Metabolic Pathways ◽

Phylogenetic Analyses ◽

Sulfate Reducing Bacteria ◽

Sulfate Reducing ◽

Hydrocarbon Emission ◽

Costa Rica Margin ◽

Reducing Bacteria ◽

Electron Transfers ◽

Deep Sediments

AbstractDeep sediments host many archaeal lineages, including the Asgard superphylum which contains lineages predicted to require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and the co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Phylogenetic analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore have the capacity to transfer the reducing equivalents (in the forms of hydrogen and formate) generated from alkane oxidation to external partners. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilization and could facilitate electron transfers from other organisms by means of these reduced substances. Their co-occurrence and metabolic features suggest that Helarchaeota may metabolize synergistically with some SRB, and together exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.

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Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

Scientific Reports ◽

10.1038/s41598-020-80690-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hongru Su ◽

Eri Onoda ◽

Hitoshi Tai ◽

Hiromi Fujita ◽

Shigetoshi Sakabe ◽

...

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

Core Genome ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Housekeeping Genes ◽

Pcr Screening ◽

Taxonomic Profiling ◽

Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

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Citrobacter tructae sp. nov. Isolated from Kidney of Diseased Rainbow Trout (Oncorhynchus mykiss)

Microorganisms ◽

10.3390/microorganisms9020275 ◽

2021 ◽

Vol 9 (2) ◽

pp. 275

Author(s):

Won Joon Jung ◽

Hyoun Joong Kim ◽

Sib Sankar Giri ◽

Sang Guen Kim ◽

Sang Wha Kim ◽

...

Keyword(s):

Rainbow Trout ◽

Oncorhynchus Mykiss ◽

Biochemical Characterization ◽

Antibiotic Resistance Genes ◽

Housekeeping Genes ◽

Rrna Gene ◽

Bacterial Identification ◽

Rainbow Trout Oncorhynchus Mykiss ◽

The 16S Rrna Gene ◽

Genome Distance

A novel Citrobacter species was isolated from the kidney of diseased rainbow trout (Oncorhynchus mykiss) reared on a trout farm. Biochemical characterization and phylogenetic analysis were performed for bacterial identification. Sequencing of the 16S rRNA gene and five housekeeping genes indicated that the strain belongs to the Citrobacter genus. However, multilocus sequence analysis, a comparison of average nucleotide identity, and genome-to-genome distance values revealed that strain SNU WT2 is distinct and forms a separate clade from other Citrobacter species. Additionally, the phenotype characteristics of the strain differed from those of other Citrobacter species. Quinone analysis indicated that the predominant isoprenoid quinone is Q-10. Furthermore, strain virulence was determined by a rainbow trout challenge trial, and the strain showed resistance to diverse antibiotics including β-lactams, quinolone, and aminoglycosides. The complete genome of strain SNU WT2 is 4,840,504 bp with a DNA G + C content of 51.94% and 106,068-bp plasmid. Genome analysis revealed that the strain carries virulence factors on its chromosome and antibiotic resistance genes on its plasmid. This strain represents a novel species in the genus Citrobacter for which the name C. tructae has been proposed, with SNU WT2 (=KCTC 72517 = JCM 33612) as the type strain.

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Phenotypically and Genotypically Heterogeneous Strains of Pseudomonas syringae Associated With Alfalfa Leaf Spot Disease in Iran

Plant Disease ◽

10.1094/pdis-06-19-1153-re ◽

2019 ◽

Vol 103 (12) ◽

pp. 3199-3208 ◽

Cited By ~ 2

Author(s):

Maryam Ansari ◽

S. Mohsen Taghavi ◽

Sadegh Zarei ◽

Soraya Mehrb-Moghadam ◽

Hamzeh Mafakheri ◽

...

Keyword(s):

Host Range ◽

Pseudomonas Syringae ◽

Leaf Spot ◽

Phylogenetic Analyses ◽

Housekeeping Genes ◽

Pcr Primers ◽

Phylogenetic Position ◽

Leaf Spot Disease ◽

Bacterial Strains ◽

Alfalfa Leaf

In this study, we provide a polyphasic characterization of 18 Pseudomonas spp. strains associated with alfalfa leaf spot symptoms in Iran. All of the strains were pathogenic on alfalfa, although the aggressiveness and symptomology varied among the strains. All strains but one were pathogenic on broad bean, cucumber, honeydew, and zucchini, whereas only a fraction of the strains were pathogenic on sugar beet, tomato, and wheat. Syringomycin biosynthesis genes (syrB1 and syrP) were detected using the corresponding PCR primers in all of the strains isolated from alfalfa. Phylogenetic analyses using the sequences of four housekeeping genes (gapA, gltA, gyrB, and rpoD) revealed that all of the strains except one (Als34) belong to phylogroup 2b of P. syringae sensu lato, whereas strain Als34 placed within phylogroup 1 close to the type strain of P. syringae pv. apii. Among the phylogroup 2b strains, nine strains were phylogenetically close to the P. syringae pv. aptata clade, whereas the remainder were scattered among P. syringae pv. atrofaciens and P. syringae pv. syringae strains. Pathogenicity and host range assays of the bacterial strains evaluated in this study on a set of taxonomically diverse plant species did not allow us to assign a “pathovar” status to the alfalfa strains. However, these results provide novel insight into the host range and phylogenetic position of the alfalfa-pathogenic members of P. syringae sensu lato, and they reveal that phenotypically and genotypically heterogeneous strains of the pathogen cause bacterial leaf spot of alfalfa.

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Meliola mangiferae. [Descriptions of Fungi and Bacteria].

IMI Descriptions of Fungi and Bacteria ◽

10.1079/dfb/20056401355 ◽

1998 ◽

Author(s):

M. Rodríguez

Keyword(s):

Puerto Rico ◽

Costa Rica ◽

Geographical Distribution ◽

Mangifera Indica ◽

British Guiana ◽

Disease Symptoms ◽

The Family

Abstract A description is provided for Meliola mangiferae. Information is included on the disease caused by the organism, its transmission, geographical distribution, and hosts. DISEASE: Meliola mangiferae, as with the family Meliolaceae in general, is found on living leaves parasitizing the epidermis and sometimes deeper tissues, but without production of obvious disease symptoms. HOSTS: Mangifera indica, M. rigida and Mangifera sp. (Hansford, 1961). GEOGRAPHICAL DISTRIBUTION: Brazil, British Guiana, Costa Rica, Cuba, India, Indonesia (Java), Jamaica, Malaysia, Panama, Philippines, Puerto Rico, Surinam, Trinidad & Tobago, Venezuela. Meliola mangiferae is found in practically all areas of mango cultivation, with the exception of Africa and Australia (Hansford, 1961). TRANSMISSION: By air-borne ascospores.

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Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar

International Journal of Molecular Sciences ◽

10.3390/ijms222413366 ◽

2021 ◽

Vol 22 (24) ◽

pp. 13366

Author(s):

Xuechun Wang ◽

Nan Chao ◽

Aijing Zhang ◽

Jiaqi Kang ◽

Xiangning Jiang ◽

...

Keyword(s):

Gene Family ◽

Biochemical Characterization ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Lignin Biosynthesis ◽

Phenylpropanoid Pathway ◽

Biochemical Properties ◽

Phylogenetic Groups ◽

Systematic Analysis ◽

A Genome

Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We conducted a genome-wide analysis of the CSE gene family, including functional and phylogenetic analyses of CSE and CSE-like genes, using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome, and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12, might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of PoptoCSE1 (Populus tomentosa), -2 and -12 showed that PoptoCSE1 and -2 maintained CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression patterns and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides a systematic understanding of this novel gene family and suggests the function of CSE in monolignol biosynthesis in Populus.

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'Candidatus Phytoplasma sacchari’, a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004591 ◽

2020 ◽

Author(s):

Kiran Kirdat ◽

Bhavesh Tiwarekar ◽

Vipool Thorat ◽

Shivaji Sathe ◽

Yogesh Shouche ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Indian Subcontinent ◽

Phylogenetic Analyses ◽

Draft Genome ◽

Housekeeping Genes ◽

Rrna Gene ◽

Genome Sequences ◽

Phytoplasma Strain ◽

White Leaf

Sugarcane Grassy Shoot (SCGS) disease is known to be related to Rice Yellow Dwarf (RYD) phytoplasmas (16SrXI-B group) which are found predominantly in sugarcane growing areas of the Indian subcontinent and South-East Asia. The 16S rRNA gene sequences of SCGS phytoplasma strains belonging to the 16SrXI-B group share 98.07 % similarity with ‘Ca. Phytoplasma cynodontis’ strain BGWL-C1 followed by 97.65 % similarity with ‘Ca. P. oryzae’ strain RYD-J. Being placed distinctly away from both the phylogenetically related species, the taxonomic identity of SCGS phytoplasma is unclear and confusing. We attempted to resolve the phylogenetic positions of SCGS phytoplasma based on the phylogenetic analysis of 16S rRNA gene (>1500 bp), nine housekeeping genes (>3500 aa), core genome phylogeny (>10 000 aa) and OGRI values. The draft genome sequences of SCGS phytoplasma (strain SCGS) and Bermuda Grass White leaf (BGWL) phytoplasma (strain LW01), closely related to ‘Ca. P. cynodontis’, were obtained. The SCGS genome was comprised of 29 scaffolds corresponding to 505 173 bp while LW01 assembly contained 21 scaffolds corresponding to 483 935 bp with the fold coverages over 330× and completeness over 90 % for both the genomes. The G+C content of SCGS was 19.86 % while that of LW01 was 20.46 %. The orthoANI values for the strain SCGS against strains LW01 was 79.42 %, and dDDH values were 22. Overall analysis reveals that SCGS phytoplasma forms a distant clade in RYD group of phytoplasmas. Based on phylogenetic analyses and OGRI values obtained from the genome sequences, a novel taxon ‘Candidatus Phytoplasma sacchari’ is proposed.

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IDENTIFICACIÓN DE TRIPS (THYSANOPTERA: THRIPIDAE) EN EL CULTIVO DE MANGO (Mangifera indica L.) EN COSTA RICA

Alcances Tecnológicos ◽

10.35486/at.v3i1.125 ◽

2019 ◽

Vol 3 (1) ◽

pp. 48-53

Author(s):

Ruth León ◽

Jimmy Gamboa ◽

Ricardo Elizondo

Keyword(s):

Costa Rica ◽

Mangifera Indica

Durante los años 2000 a 2002, se realizaron recolectas de trips asociados al cultivo demango. Se identificaron ocho especies de trips, Haplotrips gowdeyi Franklin, Frankliniellagossypiana Hood, Frankliniella pr. gossypiana, Frankliniella insularis, Frankliniella cubensis,Selenotrips rubrocinctus, Scirthotrips sp. y Frankliniella sp., de las cuales el mayor número son del género Frankliniella y otros del género Selenotrips. Asimismo, en algunas plantacio-nes que no se incluyeron en este trabajo se presentó Frankliniella cephalica. Este estudio permitió determinar que en las plantaciones de mango se encuentra un “complejo de trips”,del cual se conoce poco sobre la sincronización que se da entre las especies involucradas.El daño lo causan las formas no aladas o inmaduras, al tener un aparato bucal en forma deestilete con el cual succionan la savia en el fruto, provocando deformación del mismo.

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