Convenient Detection of the Citrus Greening (Huanglongbing) Bacterium ‘Candidatus Liberibacter asiaticus’ by Direct PCR from the Midrib Extract

A phloem-limited bacterium, ‘Candidatus Liberibacter asiaticus’ (Las) is a major pathogen of citrus greening (huanglongbing), one of the most destructive citrus diseases worldwide. The rapid identification and culling of infected trees and budwoods in quarantine are the most important control measures. DNA amplification including conventional polymerase chain reaction (PCR) has commonly been used for rapid detection and identification. However, long and laborious procedures for DNA extraction have greatly reduced the applicability of this method. In this study, we found that the Las bacterial cells in the midribs of infected leaves were extracted rapidly and easily by pulverization and centrifugation with mini homogenization tubes. We also found that the Las bacterial cells in the midrib extract were suitable for highly sensitive direct PCR. The performance of direct PCR using this extraction method was not inferior to that of conventional PCR. Thus, the direct PCR method described herein is characterized by its simplicity, sensitivity, and robustness, and is applicable to quarantine testing.     

Prophage-Mediated Dynamics of ‘Candidatus Liberibacter asiaticus’ Populations,the Destructive Bacterial Pathogens of Citrus Huanglongbing

Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus’ (Las) Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB), a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and disease development.     

Isolation of the 5′-End of Plant Genes from Genomic DNA by TATA-Box-Based Degenerate Primers

We report a rapid and simple method for isolating the 5′-end of plant genes from genomic DNA by polymerase chain reaction (PCR) with TATA-box-based degenerate primers (TDPs). The TDPs were specially designed according to the TATA box, which is conserved in the promoter region of most plant genes. The unknown 5′-ends of several genes in different plants were isolated by PCR with gene-specific primers of the known core fragment and the TDPs. Our method does not require the arduous RNA manipulations and expensive enzyme treatments of the popular rapid amplification of cDNA ends (RACE) and its variants, and so could be a cheap practical alternative.     

Isolation of Intact Chloroplasts from Spinach Leaf by Centrifugation in Gradients of the Modified Silica “Percoll”

The isolation of the photosynthetically competent chloroplast preparations was undertaken by means of the density gradient centrifugation on the modified silica sol “Percoll.” A clear separation of the intact chloroplast sustaining the high photosynthetic activities (light dependent CO₂ fixation ca. 130μmol/mg Chl·hr) was established. The contamination of mitochondria and peroxisomes was estimated to be less than 3% by measuring the activities of their marker enzymes. The chloroplasts were proved to be free from endoplasmic reticulum and cytosol. The photosynthetic CO₂ fixation of the isolated chloroplast preparations was saturated by illumination of the light intensity of 20,000 Lux (12 mW/cm², 400~750 nm).     

Infection Density Dynamics of the Citrus Greening Bacterium “Candidatus Liberibacter asiaticus” in Field Populations of the Psyllid Diaphorina citri and Its Relevance to the Efficiency of Pathogen Transmission to Citrus Plants

Huanglongbing, or citrus greening, is a devastating disease of citrus plants recently spreading worldwide, which is caused by an uncultivable bacterial pathogen, “Candidatus Liberibacter asiaticus,” and vectored by a phloem-sucking insect, Diaphorina citri. We investigated the infection density dynamics of “Ca. Liberibacter asiaticus” in field populations of D. citri with experiments using field-collected insects to address how “Ca. Liberibacter asiaticus” infection density in the vector insect is relevant to pathogen transmission to citrus plants. Of 500 insects continuously collected from “Ca. Liberibacter asiaticus”-infected citrus trees with pathological symptoms in the spring and autumn of 2009, 497 (99.4%) were “Ca. Liberibacter asiaticus” positive. The infections were systemic across head-thorax and abdomen, ranging from 10³ to 10⁷ bacteria per insect. In spring, the infection densities were low in March, at ∼10³ bacteria per insect, increasing up to 10⁶ to 10⁷ bacteria per insect in April and May, and decreasing to 10⁵ to 10⁶ bacteria per insect in late May, whereas the infection densities were constantly ∼10⁶ to 10⁷ bacteria per insect in autumn. Statistical analysis suggested that several factors, such as insect sex, host trees, and collection dates, may be correlated with “Ca. Liberibacter asiaticus” infection densities in field D. citri populations. Inoculation experiments with citrus seedlings using field-collected “Ca. Liberibacter asiaticus”-infected insects suggested that (i) “Ca. Liberibacter asiaticus”-transmitting insects tend to exhibit higher infection densities than do nontransmitting insects, (ii) a threshold level (∼10⁶ bacteria per insect) of “Ca. Liberibacter asiaticus” density in D. citri is required for successful transmission to citrus plants, and (iii) D. citri attaining the threshold infection level transmits “Ca. Liberibacter asiaticus” to citrus plants in a stochastic manner. These findings provide valuable insights into understanding, predicting, and controlling this notorious citrus pathogen.     

Bioaccumulation of Heavy Metals by Endemic Viola Species from the Soil in the Vicinity of the As-Sb-Tl Mine “Allchar”, Republic of Macedonia

Allchar mine is an abandoned arsenic-antimony-thallium deposit located on the north-western part of Ko?uf Mt., Republic of Macedonia. Allchar is a unique deposit within the world, due to the variety of its mineral composition especially and in the high content of thallium. The aim of this work was to assess the level of contamination at this post-mining area as well as to determine the intensity of accumulation of various elements (Ag, Al, As, Ba, Ca, Cd, Co, Cr, Cu, Fe, Ga, K, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Rb, S, Sb, Sr, Tl, V, and Zn) with focus on As, Sb and Tl, in two endemic Viola species from this locality (Viola allcharensis G. Beck, Viola arsenica G. Beck) and one Balkan endemic species (Viola macedonica Boiss. &; Heldr.). Samples of different plant parts and soil were digested and then analysed by ICP-AES. It was found that the accumulation of As, Sb, and Tl in these endemic species is significantly high. In this study a systematic investigation of the As-Sb-Tl contamination of soils and their bioavailability was carried out using the extraction procedure in order to explore the mobility and potential bioavailability of the As, Sb, and Tl.     

Genetic Differentiation of Three Sympatric Charr Species from the Genus SalvelinusInferred from PCR–RFLP Analysis of Mitochondrial DNA

We examined differentiation of three sympatric charr species Dolly Varden charr Salvelinus malmaWalbaum, white-spotted charrS.leucomaenisPallas, and Levanidov charrS. levanidovi Chereshnev, Scopetz, Gudkov. Using restriction fragment length polymorphism analysis (RFLP), three mitochondrial DNA fragments (ND1/ND2, ND5/ND6, and Cytb/D-loop) amplified in PCR were compared. The divergence of mtDNA nucleotide sequences betweenS. levanidovi and S. leucomaenis was about 9.7%, between S. levanidovi and S. malma, 8.7%, and between S. malma andS. laecomaenis, 7.5%. These results indicate genetic isolation of the species examined and support the earlier suggestion on closeness of Levanidov charr to the common ancestor of the genus Salvelinus.     

Characterization of “Candidatus Liberibacter Asiaticus” Populations by Double-Locus Analyses

“Candidatus Liberibacter asiaticus” (CaLas) is associated with citrus Huanglongbing (HLB, yellow shoot disease), which is highly destructive to world citrus production. Understanding the relationships of CaLas isolates from different geographical regions is important for HLB research and development of disease management strategies. In this study, 301 CaLas isolates [85 Brazil, 132 China, and 84 U.S. (83 Florida and 1 California)] were collected, and genomic variations among them were evaluated based on the analyses of two genomic loci: trn1, characteristic of variable tandem repeat numbers (TRNs), and snp1, characteristic of single nucleotide polymorphisms (SNPs). Locus trn1 revealed the homogeneity of all Brazilian isolates, and locus snp1 revealed the homogeneity of most Florida isolates. When the two loci were analyzed simultaneously, i.e., double-locus (DL) analyses, CaLas isolates were clustered mostly according to geographical origins. DL genotype 1 included 97 % of the Chinese isolates, DL genotype 2 included all Brazilian isolates, and DL genotype 3 included 93 % of the U.S. isolates. DL analyses successfully revealed inter-continental overlapping or movement pattern of CaLas isolates. The isolate recently found in California belonged to Asiatic DL genotype 1.     

XoxF-Type Methanol Dehydrogenase from the Anaerobic Methanotroph “Candidatus Methylomirabilis oxyfera”

“Candidatus Methylomirabilis oxyfera” is a newly discovered anaerobic methanotroph that, surprisingly, oxidizes methane through an aerobic methane oxidation pathway. The second step in this aerobic pathway is the oxidation of methanol. In Gram-negative bacteria, the reaction is catalyzed by pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH). The genome of “Ca. Methylomirabilis oxyfera” putatively encodes three different MDHs that are localized in one large gene cluster: one so-called MxaFI-type MDH and two XoxF-type MDHs (XoxF1 and XoxF2). MxaFI MDHs represent the canonical enzymes, which are composed of two PQQ-containing large (α) subunits (MxaF) and two small (β) subunits (MxaI). XoxF MDHs are novel, ecologically widespread, but poorly investigated types of MDHs that can be phylogenetically divided into at least five different clades. The XoxF MDHs described thus far are homodimeric proteins containing a large subunit only. Here, we purified a heterotetrameric MDH from “Ca. Methylomirabilis oxyfera” that consisted of two XoxF and two MxaI subunits. The enzyme was localized in the periplasm of “Ca. Methylomirabilis oxyfera” cells and catalyzed methanol oxidation with appreciable specific activity and affinity (V_max of 10 μmol min⁻¹ mg⁻¹ protein, K_m of 17 μM). PQQ was present as the prosthetic group, which has to be taken up from the environment since the known gene inventory required for the synthesis of this cofactor is lacking. The MDH from “Ca. Methylomirabilis oxyfera” is the first representative of type 1 XoxF proteins to be described.     

Isolation and Characterization of Oligosaccharides from the Hydrolyzate of Larch Wood Glucomannan with Endo-β-d-Mannanase

The glucomannan isolated from larch holocellulose was hydrolyzed by a purified endo-d-β-mannanase. The products were fractionated by gel filtration on a Polyacrylamide gel in water and partition chromatography on ion exchange resins in 80% ethanol. The following oligosaccharides were isolated and identified: (a) 4-O-β-d-Manp-d-Man, (b) 4-O-β-d-Glcp-d-Man, (c) 4-O-β-d-Glcp-d-Glc, (d) O-β-d-Manp-(1 →4)-O-β-d-Manp-(1 →4)-d-Man, (e) O-β-dGlcp-(l →4)-O-β-d-Manp-(l →4)-d-Man, (f) O-β-d-Manp-(l →4)-Oβ-d-Glcp-(l →4)-d-Man, (g) O-β-d-Manp-(l →4)-O-[α-d-Galp-(l →6)]-d-Man, (h) O-β-d-Manp-(l →4)-O-β-d-Manp-(l →4)-O-β-d-Manp-(l →4)-d-Man, and (i) O-β-d-Glcp-(1 →4)-O-β-d-Manp-(1 →4)-O-β-d-Manp-(1 →4)-d-Man.     

The Carbohydrate-containing Cell-Wall Polymers of Certain Species from the Cluster “Streptomyces lavendulae”

The type strains of the species of the cluster Streptomyces lavendulae with a low level of DNA–DNA relatedness were found to contain different cell-wall carbohydrate polymers, whereas the species of this cluster with a level of DNA–DNA relatedness of about 60% contain similar or identical carbohydrate polymers. The type strains Streptomyces katraeVKM Ac-1220^Tand S. polychromogenesVKM Ac-1207^Tsynthesize mannan with different amounts of -1,2- and -1,3-substituted mannopyranose units and a small number of 1,3-poly(glycerolphosphate) chains. The cell walls of S. lavendulocolorVKM Ac-215^Tand Streptomycessp. VKM Ac-2117 were found to contain a hitherto unknown teichuronic acid, whose repeating unit is a disaccharide consisting of diaminomannuronic acid and N-acetylgalactosamine: 4)--D-ManpNAc3NAcA-(1 3)--D-GalpNAc-(1 . In addition, the cell walls of these two streptomycetes contain -glucosylated 1,5-poly(ribitol phosphate). The cell walls of S. virginiaeVKM Ac-1218^Tand S. flavotriciniVKM Ac-1277^Tcontain the same poly(glucosyl-glycerolphosphate). The results presented in this paper are in accordance with the DNA–DNA relatedness data and indicate a taxonomic significance of the structure of the cell-wall polysaccharides for the delineation of phenetically related Streptomycesspecies.     

Isolation of protoplasts by means of a “species-specific” autolysine inChlamydomonas

Summary Prior to fusion, gametes ofChlamydomonas reinhardii discard their cell walls. This naturally occuring phenomenon has provided the basis for a method of protoplast isolation from both gametes and vegetative cells within the genusChlamydomonas. When synchronized cultures of compatibleChlamydomonas gametes are mixed it is possible, after removal of the cells, to obtain a solution having a high cell wall lytic activity. That vegetative and gamete cells after treatment with this gamete-autolysine are indeed protoplasts has been proved by various light and electron microscopical methods.The species specifity of this autolysine, its difference to the previously described sporangialautolysine (Schlösser 1966) and furthermore its use in the large scale production of protoplasts is also described. Since this wall autolysine is a factor produced by the cells themselves at a particular stage in their life cycle it represents a non-foreign agent in contrast to all other enzymic methods previously employed for protoplast isolation.     

Isolation of the sesquiterpene alcohol (−)-pacifigorgiol from valeriana officinalis

A tertiary bicyclic sesquiterpene alcohol has been isolated from Valeriana officinalis, and identified as (−)-pacifigorgiol, the optical antipode of the alcohol isolated from Pacifigorgia adamsii.