Characterization of blackleg and soft rot from potato in northern Thailand

Blackleg and soft rot of potato cause economic loss through reduced yield and quality. The causal agents of bacterial blackleg and soft rot of potato were identified based on biological data and sequence analyses of the 16S rDNA gene. Between 2016 and 2018, diseased potato stems and tubers were collected in Chai Prakan District, Chiang Mai Province, and Chiang Khum District, Pa Yao Province. The symptoms included black stem lesions, soft rot on tubers, wilting, break down of the stem vascular ring and foliar yellowing. Of 13 bacterial isolates, five were identified as Pectobacterium carotovorum subsp. brasiliense, four‐Dickeya dadantii, two‐Pseudomonas putida and two‐Bacillus altitudinis. Pathogenicity tests of P. carotovorum subsp. brasiliense and D. dadantii resulted in lower leaves turning yellow and wilting followed by blackleg symptoms on lower stems and maceration of tuber tissue. Symptoms caused by P. putida were yellowing and wilting of leaves. B. altitudinis caused yellowing of the lower leaves and wilting followed by drying of leaf tissue. This is a first report of these bacterial pathogens causing blackleg and soft rot of potato in Thailand.     

Molecular Characterization of Phytoplasmas Associated with Potato Purple Top Disease in Iran

Potato plants with symptoms suggestive of potato purple top disease (PPTD) occurred in the central, western and north‐western regions of Iran. Polymerase chain reaction (PCR) and nested PCR assays were performed using phytoplasma universal primer pair P1/P7 followed by primer pairs R16F2n/R16R2 and fU5/rU3 for phytoplasma detection. Using primer pairs R16F2n/R16R2 and fU5/rU3 in nested PCR, the expected fragments were amplified from 53% of symptomatic potatoes. Restriction fragment length polymorphism (RFLP) analysis using AluI, CfoI, EcoRI, KpnI, HindIII, MseI, RsaI and TaqI restriction enzymes confirmed that different phytoplasma isolates caused PPTD in several Iranian potato‐growing areas. Sequences analysis of partial 16S rRNA gene amplified by nested PCR indicated that ‘Candidatus Phytoplasma solani’, ‘Ca. Phytoplasma astris’ and ‘Ca. Phytoplasma trifolii’ are prevalent in potato plants showing PPTD symptoms in the production areas of central, western and north‐western regions of Iran, although ‘Ca. Phytoplasma solani’ is more prevalent than other phytoplasmas. This is the first report of phytoplasmas related to ‘Ca. Phytoplasma astris’, ‘Ca. Phytoplasma solani’ and ‘Ca. Phytoplasma trifolii’ causing PPTD in Iran.     

Pre-PCR Processes in the Molecular Detection of Blackleg and Soft Rot Erwiniae in Seed Potatoes

The polymerase chain reaction (PCR) based detection of blackleg and soft rot erwiniae involves pre‐PCR processing steps which may compromise the sensitivity of detection. The aim of this study was to standardize these various steps to develop reproducible diagnostic PCR protocol for the detection of the three known soft rot erwiniae as they occur in the tuber, singly or in combination. Comparison of tuber peel and stolon end tissue as a starting material for enrichment of the bacteria indicated that tuber peel samples resulted in more representative and sensitive detection of the strains than extract from stolon end tissues. Substances of potato origin in the peel extract were found to be highly inhibitory to the PCR. Addition of the antioxidant Dethiotreitol to the samples before enrichment did not have any significant effect on detection during the 24 h period incubation of the peel extract at room temperature. Bulk washing of tubers with one rotten tuber included with the working sample caused surface contamination on 67–91% of the healthy tubers. Washing tubers individually circumvents the problem. The optimum temperature for enrichment of all the three strains was 27°C. At 37°C, Pectobacterium carotovorum failed to be detected while PCR on Pectobacterium atrosepticum and isolates of Dickeya spp. always produced amplification of the specific DNA fragments. Viability test on Nutrient Agar showed that only Dickeya isolates were viable after 48 h of incubation at 37°C suggesting that the detection of P. atrosepticum at 37°C was from dead or non‐viable cells. Post cell death detection experiment further confirmed that DNA was amplified from dead cells of all the strains at 27°C and 33°C whereas at 37°C, only DNA from dead cells of isolates of Dickeya and P. atrosepticum were amplified. There was no amplification from the dead cells of all isolates of P. carotovorum following the 48 h post death incubation at 37°C. The reason for this difference in post death longevity is not clear at this stage.     

Molecular Characterization of a Phytoplasma Associated with Potato Witches’‐broom Disease in Iran

Potato plants showing symptoms suggestive of potato witches’‐broom disease including witches’‐broom, little leaf, stunting, yellowing and swollen shoots formation in tubers were observed in the central Iran. For phytoplasma detection, Polymerase Chain Reaction (PCR) and nested PCR assays were performed using phytoplasma universal primer pair P1/P7, followed by primer pair R16F2n/R16R2. Random fragment length polymorphism analysis of potato phytoplasma isolates collected from different production areas using the CfoI restriction enzyme indicated that potato witches’‐broom phytoplasma isolate (PoWB) is genetically different from phytoplasmas associated with potato purple top disease in Iran. Sequence analysis of the partial 16S rRNA gene amplified by nested PCR indicated that ‘Candidatus Phytoplasma trifolii’ is associated with potato witches’‐broom disease in Iran. This is the first report of potato witches’‐broom disease in Iran.     

Molecular Characterization of Phytoplasmas Associated with Peach Diseases in Iran

Recently, peach trees showing leaf rolling, little leaf, rosetting, yellowing, bronzing of foliage and tattered and shot‐holed leaves symptoms were observed in peach growing areas in the central and north‐western regions of Iran. Polymerase chain reaction (PCR) and nested PCR using phytoplasma universal primer pairs P1/Tint, R16F2/R2, PA2F/R and NPA2F/R were employed to detect phytoplasmas. The nested PCR assays detected phytoplasma infections in 51% of symptomatic peach trees in the major peach production areas in East Azerbaijan, Isfahan, ChaharMahal‐O‐Bakhtiari and Tehran provinces. Restriction fragment length polymorphism (RFLP) analyses of 485 bp fragments amplified using primer pair NPA2F/R in nested PCR revealed that the phytoplasmas associated with infected peaches were genetically different and they were distinct from phytoplasmas that have been associated with peach and almond witches’‐broom diseases in the south of Iran. Sequence analyses of partial 16S rDNA and 16S–23S rDNA intergenic spacer regions demonstrated that ‘Candidatus Phytoplasma aurantifolia’, ‘Ca. Phytoplasma solani’ and ‘Ca. Phytoplasma trifolii’ are prevalent in peach growing areas in the central and north‐western regions of Iran.     

Salicylic and jasmonic acid pathways are necessary for defence against Dickeya solani as revealed by a novel method for Blackleg disease screening of in vitro grown potato

Potato is major crop ensuring food security in Europe, and blackleg disease is increasingly causing losses in yield and during storage. Recently, one blackleg pathogen, Dickeya solani has been shown to be spreading in Northern Europe that causes aggressive disease development. Currently, identification of tolerant commercial potato varieties has been unsuccessful; this is confounded by the complicated etiology of the disease and a strong environmental influence on disease development. There is currently a lack of efficient testing systems. Here, we describe a system for quantification of blackleg symptoms on shoots of sterile in vitro potato plants, which saves time and space compared to greenhouse and existing field assays. We found no evidence for differences in infection between the described in vitro‐based screening method and existing greenhouse assays. This system facilitates efficient screening of blackleg disease response of potato plants independent of other microorganisms and variable environmental conditions. We therefore used the in vitro screening method to increase understanding of plant mechanisms involved in blackleg disease development by analysing disease response of hormone‐ related (salicylic and jasmonic acid) transgenic potato plants. We show that both jasmonic (JA) and salicylic (SA) acid pathways regulate tolerance to blackleg disease in potato, a result unlike previous findings in Arabidopsis defence response to necrotrophic bacteria. We confirm this by showing induction of a SA marker, pathogenesis‐related protein 1 (StPR1), and a JA marker, lipoxygenase (StLOX), in Dickeya solani infected in vitro potato plants. We also observed that tubers of transgenic potato plants were more susceptible to soft rot compared to wild type, suggesting a role for SA and JA pathways in general tolerance to Dickeya.     

Finding of 132, 173‐cyclopheophorbide a enol as a degradation product of chlorophyll in shrunk zooxanthellae of the coral Montipora digitata

We examined the morphology and pigment composition of zooxanthellae in corals subjected to normal temperature (27°C) and thermal stress (32°C). We observed several normal and abnormal morphological types of zooxanthellar cells. Normal cells were intact and their chloroplasts were unbroken (healthy); abnormal cells were shrunken and had partially degraded or broken chloroplasts, or they were bleached and without chloroplasts. At 27°C, most healthy zooxanthellar cells were retained in the coral tissue, whereas shrunken zooxanthellae were expelled. Under thermal stress, the abundance of healthy zooxanthellae declined and the proportion of shrunken/abnormal cells increased in coral tissues. The rate of algal cell expulsion was reduced under thermal stress. Within the shrunken cells, we detected the presence of a chl‐like pigment that is not ordinarily found in healthy zooxanthellae. Analysis of the absorption spectrum, absorption maxima, and retention time (by HPLC) indicated that this pigment was 13², 17³‐cyclopheophorbide a enol (cPPB‐aE), which is frequently found in marine and lacustrine sediments, and in protozoans that graze on phytoplankton. The production of cPPB‐aE in shrunken zooxanthellae suggests that the chls have been degraded to cPPB‐aE, a compound that is not fluorescent. The lack of a fluorescence function precludes the formation of reactive oxygen species. We therefore consider the formation of cPPB‐aE in shrunken zooxanthellae to be a mechanism for avoiding oxidative stress.     

Niger Seed (Guizotia abyssinica), a New Host of ‘Candidatus Phytoplasma asteris’ in Iran

Shrubs of niger seed with phyllody and internode elongation symptoms suggestive of phytoplasma infections occurred in the central regions of Iran. Phytoplasma was detected by polymerase chain reaction (PCR) and nested PCR amplifications using phytoplasma universal primer pairs P1/P7 and R16F2n/R16R2. Using aster yellows group–specific primer pair rp(I)F1A/rp(I)R1A, a fragment of 1212 bp of the rp genes was amplified from DNA samples of infected plants. Random fragment length polymorphism (RFLP) analyses of R16F2n/R16R2‐amplified products using the CfoI restriction enzyme confirmed that Iranian niger seed phyllody phytoplasma is associated with aster yellows group phytoplasmas. Sequence analyses of the partial rp genes fragment indicated that the Iranian niger seed phyllody phytoplasma, which was collected from central regions of Iran, is related to ‘Candidatus Phytoplasma asteris’. This is the first report of a phytoplasma infecting the niger seed plant.     

Detection and Molecular Identification of Aster Yellows Phytoplasma in Date Palm in Egypt

Phytoplasma‐like symptoms were detected in date palm trees (Phoenix dactylifera L.) in Al‐Giza Governorate in Egypt. Symptoms varied from leaf chlorotic streaks, stunting and marked reduction in fruit and stalk sizes. Direct and nested PCR of symptomatic samples using P1/P7 and R16F2n/R16R2n primers, respectively, of the 16S rRNA gene, resulted in a DNA amplification product of c. 1.3 kbp. Symptomless samples collected from the same location and the healthy control produced no product upon amplification. Products were cloned into TOPO TA vector for sequencing. Data generated were deposited in the GenBank (Accession KF826615 ). A BLAST search showed that the sequence of the 16SrRNA gene shared ‘Candidatus Phytoplasma asteris’ (16SrI group) with other isolates. Phylogenetic analysis revealed that the isolate clustered with the date palm phytoplasma causing Al‐Wijam disease in Saudi Arabia.     

Amphibious adaptations in a newly recognized amphibious fish: Terrestrial locomotion and the influences of body size and temperature

Amphibious animals are adapted for both aquatic and terrestrial habitats. The conflicting requirements for dual habitats are perhaps most pronounced in the air‐breathing fishes, which represent an intermediate stage between the totally aquatic habitat and terrestrial colonization. A key requirement for amphibious fishes is terrestrial locomotion. The different densities and compositions of air and water impose constraints for efficient terrestrial locomotion that differ from those required for aquatic locomotion. I investigated terrestrial locomotion in a small South African fish, Galaxias ‘nebula’, by exposing 60 individual fish to air in specially designed raceways and quantifying movement type and occurrence as a function of availability of water, fish size and environmental temperature. Nebula showed a sustained undulating form of terrestrial locomotion characteristic of amphibious fishes and also a transient ballistic locomotion (jumps) typical of fully aquatic species. Terrestrial movement was influenced by fish size, with medium‐sized fish undertaking more jumps towards water, and fewer jumps away from water, than their smaller or larger conspecifics. In contrast, axial undulation was mainly influenced by temperature. However, there was no consistent pattern in temperature effects presumably because temperature is just one of a suit of environmental factors that may affect terrestrial locomotion. Nebula's amphibious adaptations allow it to cope with the unpredictability inherent in its natural environment.     

Genotypic and Pathotypic Diversity of Xanthomonas oryzae pv. oryzae Strains in Taiwan

Rice bacterial leaf blight, caused by Xanthomonas oryzae pv. oryzae [(Ishiyama) Swings et al. 1990] (Xoo), is a major rice disease of the second crop season in Taiwan. A total of 88 Xoo strains collected from 10 major rice cultivating areas in Taiwan from 1986, 1997, 2000, 2004, and 2011 were characterized by repetitive‐element PCR (REP‐PCR) fingerprinting and virulence analyses. Among the five genetic clusters identified by the pJEL1/pJEL2 (IS1112‐based) and REP1R‐Dt/REP2‐D [repetitive extragenic palindromic (REP)‐based] primer sets, clusters A, C and D contained Xoo strains from geographically distant regions, which suggests a high frequency of Xoo dispersal in Taiwan. The 88 Xoo strains were evaluated by inoculations on IRBB near‐isogenic lines and five Taiwan rice cultivars. A subset of 45 moderately or highly virulent strains were classified into 15 pathotypes by their compatible or incompatible reactions on IR24 and 12 IRBB near‐isogenic lines, each containing a single resistance gene. Analysis of molecular haplotypes and pathotypes revealed a partial relationship. IRBB5, IRBB21 and IRBB4 were incompatible with 96%, 96% and 73% of the strains, so xa5, Xa21 and Xa4 can recognize most of the Xoo strains in Taiwan and elicit resistance. In contrast, IRBB3 (Xa3), IRBB8 (xa8), IRBB10 (Xa10), IRBB11 (Xa11), IRBB13 (xa13) and IRBB14 (Xa14) were susceptible to almost all of the 45 Xoo strains. Inoculation trials revealed significant differences in the susceptibility of five Taiwan cultivars to Xoo (from high to low susceptibility: Taichung Sen 10 >  IR24, Taichung Native 1 >  Taichung 192, Taikeng 9, Tainan 11). This study provides useful information for resistance breeding and the development of disease management strategies against bacterial blight disease of rice.     

A lethal ovitrap‐based mass trapping scheme for dengue control in Australia: I. Public acceptability and performance of lethal ovitraps

We report on the first field evaluation of the public acceptability and performance of two types of lethal ovitrap (LO) in three separate trials in Cairns, Australia. Health workers were able to set standard lethal ovitraps (SLOs) in 75 and 71% of premise yards in the wet and dry season, respectively, and biodegradable lethal ovitraps (BLOs) in 93% of yards. Public acceptance, measured as retention of traps by residents, was high for both trap types, with <9% of traps missing after 4 weeks. Traps retaining water after 4 weeks were 78 and 34% for the two SLO trials and 58% for the BLOs. The ‘failure rate’ in the 535 BLOs set in the field for 4 weeks was 47%, of which 19% were lost, 51% had holes from probable insect chewing, 23% were knocked over, 7% had dried by evaporation and 1% were split. There was no significant difference in the failure rate of BLOs set on porous (grass, soil and mulch) versus solid (tiles, concrete, wood and stone) substrates. The SLOs and the BLOs were readily acceptable to ovipositing Aedes aegypti L. (Diptera: Culicidae); the mean number of eggs/trap was 6 and 15, for the dry season and wet season SLO trial, respectively, and 15 for the BLO wet season trial. Indeed, 84–94% of premise yards had egg positive SLOs or BLOs. A high percentage of both wet and dry season SLOs (29 and 70%, respectively) and BLOs (62%) that were dry after 4 weeks were egg positive, indicating the traps had functioned. Lethal strips from SLOs and BLOs that had been exposed for 4 weeks killed 83 and 74%, respectively, of gravid Ae. aegypti in laboratory assays. These results indicate that mass trapping schemes using SLOs and BLOs are not rejected by the public and effectively target gravid Ae. aegypti. The impact of the interventions on mosquito populations is described in a companion paper.     

Genome of ‘Charleston Gray’, the principal American watermelon cultivar,and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.     

A lethal ovitrap‐based mass trapping scheme for dengue control in Australia: II. Impact on populations of the mosquito Aedes aegypti

In Cairns, Australia, the impacts on Aedes aegypti L. (Diptera: Culicidae) populations of two types of ‘lure & kill’ (L&K) lethal ovitraps (LOs), the standard lethal ovitrap (SLO) and the biodegradable lethal ovitrap (BLO) were measured during three mass‐trapping interventions. To assess the efficacy of the SLO, two interventions (one dry season and one wet season) were conducted in three discrete areas, each lasting 4 weeks, with the following treatments: (i) SLOs (>200 traps, ∼4/premise), BG‐sentinel traps (BGSs; ∼15, 1/premise) and larval control (container reduction and methoprene treatment) and (ii) larval control alone, and (iii) untreated control. Female Ae. aegypti populations were monitored for 4 weeks pre‐ and post‐treatment in all three areas using BGSs and sticky ovitraps (SOs) or non‐lethal regular ovitraps (ROs). In the dry season, 206 SLOs and 15 BGSs set at 54 and 15 houses, respectively, caught and killed an estimated 419 and 73 female Ae. aegypti, respectively. No significant decrease in collection size of female Ae. aegypti could be attributed to the treatments. In the wet season, 243 SLOs and 15 BGSs killed ∼993 and 119 female Ae. aegypti, respectively. The mean number of female Ae. aegypti collected after 4 weeks with SOs and BGSs was significantly less than the control (LSD post‐hoc test). The third mass‐trapping intervention was conducted using the BLO during the wet season in Cairns. For this trial, three treatment areas were each provided with BLOs (>500, ∼4/premise) plus larval control, and an untreated control area was designated. Adult female Ae. aegypti were collected for 4 weeks pre‐ and post‐treatment using 15 BGSs and 20 SOs. During this period, 53.2% of BLOs contained a total of 6654 Ae. aegypti eggs. Over the intervention period, collections of Ae. aegypti in the treatment areas were significantly less than in the control area for BGSs but not SOs. An influx of relatively large numbers of young females may have confounded the measurement of changes in populations of older females in these studies. This is an important issue, with implications for assessing delayed action control measures, such as LOs and parasites/pathogens that aim to change mosquito age structure. Finally, the high public acceptability of SLOs and BLOs, coupled with significant impacts on female Ae. aegypti populations in two of the three interventions reported here, suggest that mass trapping with SLOs and BLOs can be an effective component of a dengue control strategy.     

A bridge too far in naming species: a total evidence approach does not support recognition of four species in Desertifilum (Cyanobacteria)

A population of Desertifilum (Cyanobacteria, Oscillatoriales) from an oligotrophic desertic biotope was isolated and characterized using a polyphasic approach including molecular, morphological, and ecological information. The population was initially assumed to be a new species based on ecological and biogeographic separation from other existing species, however, phylogenetic analyses based on sequences of the 16S rRNA gene and 16S–23S ITS region, placed this strain clearly within the type species, Desertifilum tharense. Comparative analysis of morphology, 16S rRNA gene similarity, 16S–23S ITS secondary structure, and percent dissimilarity of the ITS regions for all characterized strains supports placing the six Desertifilum strains (designated as PD2001/TDC17, UAM‐C/S02, CHAB7200, NapGTcm17, IPPAS B‐1220, and PMC 872.14) into D. tharense. The recognition of Desertifilum salkalinema and Desertifilum dzianense is not supported, although our analysis does support continued recognition of Desertifilum fontinale. Pragmatic criteria for recognition of closely related species are proposed based on this study and others, and more rigorous review of future taxonomic papers is recommended.     

Contrasting responses to Pleistocene climate changes: a case study of two sister species Allium cyathophorum and A. spicata (Amaryllidaceae) distributed in the eastern and western Qinghai–Tibet Plateau

It has been hypothesized that species occurring in the eastern and the western Qinghai–Tibet Plateau (QTP) responded differently to climate changes during the Pleistocene. Here, we test this hypothesis by phylogeographic analysis of two sister species, Allium cyathophorum and A. spicata. We sequenced two chloroplast DNA (cpDNA) fragments (accD‐psaI and the rpl16 intron) of 150 individuals, and the nuclear (ITS) region of 114 individuals, from 19 populations throughout the distributional ranges of these species. The divergence between the two species was dated at 779 ‐ 714 thousand years before the present and was likely initiated by the most major glaciation in the QTP. Analysis of chlorotype diversity showed that A. spicata, the species occurring in the western QTP, contains much lower genetic diversity (0.25) than A. cyathophorum (0.93), which is distributed in the eastern QTP. Moreover, multiple independent tests suggested that the A. spicata population had expanded recently, while no such expansion was detected in A. cyathophorum, indicating a contrasting pattern of responses to Pleistocene climate changes. These findings highlight the importance of geographical topography in determining how species responded to the climate changes that took place in the QTP during the Pleistocene.