Bakteerigenomien tutkimus

ei saatavill

Spreading of Trioza apicalis and development of "Candidatus Liberibacter solanacearum" infection on carrot in the field conditions

Carrot cultivation in Europe is suffering from infections with "Candidatus Liberibacter solanacearum" (CLso), a psyllid-transmitted bacterial pathogen. In this study, field experiments were carried out in Finland to separately measure the effects of psyllid feeding damage and CLso infection on the carrot root growth and to reveal the dynamics of the spreading of CLso within the field. Most of the experiments were carried out during the summers 2016 and 2017, and a follow-up sampling was performed in 2018. Carrot psyllid (Trioza apicalis) flight activity was monitored and carrots were sampled at 25 points within the field. Early in the season a clear spatial correlation was found between the sampling sites showing the psyllid feeding damage, that is, leaf-curling, up to the range of 40-60 m, indicating aggregation behaviour of the psyllids. No CLso infections were detected in the first sampling, which was performed before the psyllid flight peak in both years. Later, a positive correlation between the psyllid feeding damage and the CLso titre was observed. An increase in the CLso titre occurred approximately a month after the psyllid flight peak, and this increase correlated with the accumulating effective temperature sum. In 2016, both the psyllid feeding damage and CLso infection had a significant effect on the carrot root weight. The effect of CLso titre on root weight was nonlinear, that is, it intensified rapidly at the highest bacterial titres. During the colder summer of 2017 the CLso titres did not reach high enough levels in the plants to cause substantial visible symptoms and root growth reduction. Thus, it seems that in the Nordic conditions the effect of CLso infection on carrot yield is strongly dependent on the weather conditions during the growing season.Peer reviewe

Characterisation of erwinias causing blackleg and soft rot in Finland

Potato stems showing blackleg or wilting were collected during 2003-2004 and the erwinias were isolated based on cavity forming on pectate-containing media followed by anaerobic growth test. Bacteri were also isolated from rotting tubers and from water samples collected from rivers in southern and western Finland

A novel haplotype of 'Candidatus Liberibacter solanacearum' found in Apiaceae and Polygonaceae family plants

A previously unknown haplotype of the plant pathogen 'Candidatus Liberibacter solanacearum' (Lso) was found in cultivated carrots and parsnips in eastern Finland. That same haplotype was found in western Finland, over 300 km away, in the family Polygonaceae, the species Fallopia convolvulus (wild buckwheat) and Persicaria lapathifolia (pale persicaria) growing as weeds within carrot and parsnip fields. The infected plants, both apiaceous and polygonaceous, showed symptoms of foliar discolouration. This is the first report of Lso bacteria in plants of the family Polygonaceae. The finding that the polygonaceous plants infected with a previously unknown haplotype of Lso were growing among the apiaceous plants infected with Lso haplotype C suggests that these two haplotypes might be transmitted by different vectors. Phylogenetic analyses showed that the new haplotype, called haplotype H, is distinct from the previously characterized haplotypes and appears to have diverged early from their common ancestor. Multi-locus sequence analysis revealed four different sequence types (strains) within the haplotype H. These findings suggest that the haplotype H is likely to be endemic in northern Europe and that the genetic diversity within the Lso species is higher than previously assumed.Peer reviewe

Carrot Pathogen 'Candidatus Liberibacter solanacearum' Haplotype C Detected in Symptomless Potato Plants in Finland

'Candidatus Liberibacter solanacearum' (CLso) haplotype C, a bacterial pathogen transmitted by the carrot psyllid Trioza apicalis, causes yield losses in carrot production. Due to concerns that this pathogen might also threaten potato ( Solanum tuberosum) production, the occurrence of CLso in cultivated and volunteer potatoes in Tavastia Proper and Satakunta regions of Finland was studied. Volunteer potato plants were found in 13 of the 27 inspected carrot fields. Of the 148 potato samples tested by PCR, eight volunteer potato plants and one cultivated potato grown at the edge of a carrot field were found to be CLso positive. The PCR products obtained from these potatoes with primers OA2/OI2c, LpFrag4-1611F/LpFrag4-480R and CL514F/CL514R all showed 100% sequence identity to CLso haplotype C. This is the first observation of CLso haplotype C in field-grown potatoes. In addition, transmission experiments were performed. Attempts to transmit CLso into potato with carrot psyllids were not successful; however, CLso haplotype C was transmitted from infected carrots to potato plants by leaf grafting and by phloem connection formed by dodder, a parasitic plant, and found to survive in the potato plants for several weeks after transmission. However, the bacterial colonisation progressed slowly in the potato phloem and the amount of bacteria detected was low. The plants produced from the daughter tubers of the CLso-positive potato plants were all CLso negative, suggesting that CLso haplotype C was not able to pass to the daughter plants. None of the CLso-positive potatoes inoculated in greenhouse or collected from fields showed symptoms characteristic of zebra chip disease, associated with CLso haplotypes A and B.Peer reviewe

Dickeya-sukuiset bakteerit, uusi riesa perunanviljelyssä

Perunantyvi- ja märkämätä ovat perunalla esiintyviä bakteeritauteja, jotka mädättävät perunan varsientyviosia sekä perunan mukuloita pellolla ja varastossa. Näitä tauteja aiheuttavien bakteereiden esiintyminenon vakava laatuongelma varsinkin siemenperunan viljelyssä. Taudin esiintyminen heikentää luottamustakotimaisen siemenen laatuun, lisää paineita ulkomaisen siemenperunan tuontiin ja haittaa suomalaisensiemenperunan vientimahdollisuuksia. Lisäksi mukuloita pilaava märkämätä aiheuttaa vuosittain satojentuhansien kilojen varastohävikkejä etenkin ruokaperunateollisuudessa. Perunantyvi- ja märkämätääaiheuttavat bakteerit luettiin aiemmin Erwinia-sukuun, mutta niiden taksonomia on uudistettu hiljattain,minkä seurauksena ne jaetaan nykyään kahteen sukuun, Pectobacterium ja Dickeya.Pectobacterium-sukuisten bakteereiden on tiedetty jo kauan aiheuttavan tautia perunoilla Suomessa. Perunantautitilanteen on kuitenkin epäilty huonontuneen viime vuosina, minkä vuoksi perunoissa ja jokivesissäesiintyvät bakteerit kartoitettiin vuosina 2004-2007 toteutetussa tutkimuksessa. Tulokset osoittivat, että noin20% tyvimädästä johtui todennäköisesti Dickeya-sukuisista bakteereista (edelliseltä nimeltään Erwiniachrysanthemi). Näitä bakteereita on aiemmin pidetty kasvitautien aiheuttajana lämpimissä ja trooppisissamaissa. Ne ovat levinneet viime vuosina huolestuttavasti Keski-Euroopassa ja nyt niitä tavataan siis myösmeillä. Tutkimuksen tulokset osoittivat myös, että Suomesta löydetyt bakteerit voitiin jakaa kolmeenryhmään, joista kahta voitiin eristää sekä jokivesistä että perunoista ja yhtä löydettiin vain jokivesistä Etelä- jaLänsi-Suomesta. Osa sekä perunoista että jokivesistä eristetyistä kannoista oli hyvin virulentteja. Kaikkienvirulenteimmat kannat kuuluivat Dickeya dianthicola -lajiin, joka on karanteenitaudinaiheuttajakoristekasvien kasvihuoneviljelyssä. Monet eristetyt kannat aiheuttivat tyypillisiä tyvimätäoireita muttamyös nekroottisia oireita, jotka eivät muistuttaneet tyypillistä tyvimätää. Tämä saattaa aiheuttaa ongelmiakasvustotarkastuksissa, sillä uudet bakteerit saattavat jäädä niissä havaitsematta. Syyt Dickeya-sukuistentaudinaiheuttajien leviämiseen maahamme eivät ole selvät. Leviäminen saattaa olla seurausta ilmastonlämpenemisestä mutta myös lisääntyneestä maataloustuotteiden tuonnista tai bakteereiden sopeutumisestakylmempään ilmastoon

Gene expression and phytohormone levels in the asymptomatic and symptomatic phases of infection in potato tubers inoculated with Dickeya solani

Dickeya solani is a soft rot bacterium with high virulence. In potato, D. solani, like the other potato-infecting soft rot bacteria, causes rotting and wilting of the stems and rotting of tubers in the field and in storage. Latent, asymptomatic infections of potato tubers are common in harvested tubers, and if the storage conditions are not optimal, the latent infection turns into active rotting. We characterized potato gene expression in artificially inoculated tubers in nonsymptomatic, early infections 1 and 24 hours post-inoculation (hpi) and compared the results to the response in symptomatic tuber tissue 1 week (168 hpi) later with RNA-Seq. In the beginning of the infection, potato tubers expressed genes involved in the detection of the bacterium through pathogen-associated molecular patterns (PAMPs), which induced genes involved in PAMPs-triggered immunity, resistance, production of pathogenesis-related proteins, ROS, secondary metabolites and salicylic acid (SA) and jasmonic acid (JA) biosynthesis and signaling genes. In the symptomatic tuber tissue one week later, the PAMPs-triggered gene expression was downregulated, whereas primary metabolism was affected, most likely leading to free sugars fueling plant defense but possibly also aiding the growth of the pathogen. In the symptomatic tubers, pectic enzymes and cell wall-based defenses were activated. Measurement of hormone production revealed increased SA concentration and almost no JA in the asymptomatic tubers at the beginning of the infection and high level of JA and reduced SA in the symptomatic tubers one week later. These findings suggest that potato tubers rely on different defense strategies in the different phases of D. solani infection even when the infection takes place in fully susceptible plants incubated in conditions leading to rotting. These results support the idea that D. solani is a biotroph rather than a true necrotroph.Peer reviewe

Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

Background Oligogalacturonides (OGs) are important components of damage-associated molecular pattern (DAMP) signaling and influence growth regulation in plants. Recent studies have focused on the impact of long OGs (degree of polymerization (DP) from 10–15), demonstrating the induction of plant defense signaling resulting in enhanced defenses to necrotrophic pathogens. To clarify the role of trimers (trimeric OGs, DP3) in DAMP signaling and their impact on plant growth regulation, we performed a transcriptomic analysis through the RNA sequencing of Arabidopsis thaliana exposed to trimers. Results The transcriptomic data from trimer-treated Arabidopsis seedlings indicate a clear activation of genes involved in defense signaling, phytohormone signaling and a down-regulation of genes involved in processes related to growth regulation and development. This is further accompanied with improved defenses against necrotrophic pathogens triggered by the trimer treatment, indicating that short OGs have a clear impact on plant responses, similar to those described for long OGs. Conclusions Our results demonstrate that trimers are indeed active elicitors of plant defenses. This is clearly indicated by the up-regulation of genes associated with plant defense signaling, accompanied with improved defenses against necrotrophic pathogens. Moreover, trimers simultaneously trigger a clear down-regulation of genes and gene sets associated with growth and development, leading to stunted seedling growth in Arabidopsis. Keywords Plant signaling Arabidopsis thaliana Oligogalacturonides OG Trimers Transcriptomics Defense induction Growth inhibition Disease resistance Pectobacterium carotovorum Botrytis cinereaPeer reviewe

Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

Background Oligogalacturonides (OGs) are important components of damage-associated molecular pattern (DAMP) signaling and influence growth regulation in plants. Recent studies have focused on the impact of long OGs (degree of polymerization (DP) from 10–15), demonstrating the induction of plant defense signaling resulting in enhanced defenses to necrotrophic pathogens. To clarify the role of trimers (trimeric OGs, DP3) in DAMP signaling and their impact on plant growth regulation, we performed a transcriptomic analysis through the RNA sequencing of Arabidopsis thaliana exposed to trimers. Results The transcriptomic data from trimer-treated Arabidopsis seedlings indicate a clear activation of genes involved in defense signaling, phytohormone signaling and a down-regulation of genes involved in processes related to growth regulation and development. This is further accompanied with improved defenses against necrotrophic pathogens triggered by the trimer treatment, indicating that short OGs have a clear impact on plant responses, similar to those described for long OGs. Conclusions Our results demonstrate that trimers are indeed active elicitors of plant defenses. This is clearly indicated by the up-regulation of genes associated with plant defense signaling, accompanied with improved defenses against necrotrophic pathogens. Moreover, trimers simultaneously trigger a clear down-regulation of genes and gene sets associated with growth and development, leading to stunted seedling growth in Arabidopsis. Keywords Plant signaling Arabidopsis thaliana Oligogalacturonides OG Trimers Transcriptomics Defense induction Growth inhibition Disease resistance Pectobacterium carotovorum Botrytis cinereaPeer reviewe

Effect of wet storage conditions on potato tuber transcriptome, phytohormones and growth

BackgroundStored potato (Solanum tuberosum L.) tubers are sensitive to wet conditions that can cause rotting in long-term storage. To study the effect of water on the tuber surface during storage, microarray analysis, RNA-Seq profiling, qRT-PCR and phytohormone measurements were performed to study gene expression and hormone content in wet tubers incubated at two temperatures: 4 degrees C and 15 degrees C. The growth of the plants was also observed in a greenhouse after the incubation of tubers in wet conditions.ResultsWet conditions induced a low-oxygen response, suggesting reduced oxygen availability in wet tubers at both temperatures when compared to that in the corresponding dry samples. Wet conditions induced genes coding for heat shock proteins, as well as proteins involved in fermentative energy production and defense against reactive oxygen species (ROS), which are transcripts that have been previously associated with low-oxygen stress in hypoxic or anoxic conditions. Wet treatment also induced senescence-related gene expression and genes involved in cell wall loosening, but downregulated genes encoding protease inhibitors and proteins involved in chloroplast functions and in the biosynthesis of secondary metabolites. Many genes involved in the production of phytohormones and signaling were also affected by wet conditions, suggesting altered regulation of growth by wet conditions. Hormone measurements after incubation showed increased salicylic acid (SA), abscisic acid (ABA) and auxin (IAA) concentrations as well as reduced production of jasmonate 12-oxo-phytodienoic acid (OPDA) in wet tubers. After incubation in wet conditions, the tubers produced fewer stems and more roots compared to controls incubated in dry conditions.ConclusionsIn wet conditions, tubers invest in ROS protection and defense against the abiotic stress caused by reduced oxygen due to excessive water. Changes in ABA, SA and IAA that are antagonistic to jasmonates affect growth and defenses, causing induction of root growth and rendering tubers susceptible to necrotrophic pathogens. Water on the tuber surface may function as a signal for growth, similar to germination of seeds.Peer reviewe