Harri Kokko | University of Eastern Finland (original) (raw)

Papers by Harri Kokko

DOAJ (DOAJ: Directory of Open Access Journals), Mar 1, 2022

Acta Agriculturae Scandinavica Section B-soil and Plant Science, Nov 1, 2022

IV International Strawberry Symposium, 2002

Plant-derived flavonoid compounds act as protective nutrients possessing antioxidant and free rad... more Plant-derived flavonoid compounds act as protective nutrients possessing antioxidant and free radical scavenging activity in foods. An HPLC-based quantitative procedure with improved extraction and hydrolysis was used to analyse the content of the flavonols myricetin, quercetin and kaempferol in strawberry cultivars. The quercetin contents in strawberry cultivars ranged from 0.7 to 2.6 mg 100 g-1 fresh weight. The kaempferol levels ranged from 0.9 to 2.2 mg 100 g-1. In cv. Senga Sengana the amount of myricetin was hardly detectable, while in cv. Honeoye it was 1.7 mg 100 g-1. The sum of the three flavonols varied greatly among the strawberry cultivars. In general, cv. Honeoye (fairly resistant to fungal diseases) contained the highest amount of flavonols and the old cv. Senga Sengana (susceptible to fungal diseases) contained the lowest amount of flavonols. The high variability in the flavonol contents offers possible avenues for identifying and selecting strawberry genotypes rich in health-promoting compounds.

Freshwater crayfish, Apr 15, 2021

Eroded swimmeret syndrome (ESS) was first described in 2014 from Swedish signal crayfish (Pacifas... more Eroded swimmeret syndrome (ESS) was first described in 2014 from Swedish signal crayfish (Pacifastacus leniusculus (Dana)), and later also from Finland, with gross symptoms and disease agent candidates identified and described by 2015. The ESS was first discovered affecting alien signal crayfish in Fennoscandia. The ESS is caused by a multiple infection involving Aphanomyces astaci (Schikora) and Fusarium species complex (SC). The ESS symptoms include first melanised spots in swimmerets, then partial swimmeret erosion and finally loss of a swimmeret. There could be a total loss of all swimmerets in the most severe cases. Both females and males can be affected by the ESS. In females, the ESS lowers reproductive success while in males the ESS often causes erosion of the gonopods and thus possible partial failure in mating. The ESS is more frequent among mature females that have reproduced once compared to immature females or those that are mature but have not yet reproduced. The proportion of females with ESS has ranged from 10 to 50% among Lake Saimaa signal crayfish in Finland and in a wider survey from Sweden the range was from 0 to 38%. Among Lake Saimaa male signal crayfish, the ESS proportion has been less than 10%, while it was only 0.6% in the Swedish data. The ESS has also been observed among alien signal crayfish in Switzerland. There are recent observations of ESS affecting narrow-clawed crayfish, Pontastacus leptodactylus (Eschscholtz), in Croatia and Romania (i.e., among native European crayfish stocks). Here, we summarise current knowledge about the ESS and speculate on a few potentially crucial impacts of this syndrome.

Phytopathology®, 2018

The phytopathogen Phytophthora cactorum infects economically important herbaceous and woody plant... more The phytopathogen Phytophthora cactorum infects economically important herbaceous and woody plant species. P. cactorum isolates differ in host specificity; for example, strawberry crown rot is often caused by a specialized pathotype. Here we compared the transcriptomes of two P. cactorum isolates that differ in their virulence to garden strawberry (Pc407: high virulence; Pc440: low virulence). De novo transcriptome assembly and clustering of contigs resulted in 19,372 gene clusters. Two days after inoculation of Fragaria vesca roots, 3,995 genes were differently expressed between the P. cactorum isolates. One of the genes that were highly expressed only in Pc407 encodes a GAF sensor protein potentially involved in membrane trafficking processes. Two days after inoculation, elicitins were highly expressed in Pc407 and lipid catabolism appeared to be more active than in Pc440. Of the carbohydrate-active enzymes, those that degrade pectin were often more highly expressed in Pc440, wher...

Neurochemistry International, 1992

Additional file 1 Figure S1. Screenshots of Geneious alignment for the atp9-nad9 sequences of Phy... more Additional file 1 Figure S1. Screenshots of Geneious alignment for the atp9-nad9 sequences of Phytophthora species provided by Miles et al. (2015). For the P. fragariae atp9-nad9 sequence, primers and probe binding regions are annotated.

Journal of Biological Chemistry, 1992

In the present work we have investigated the macromolecules that contribute to the brain 1H NMR s... more In the present work we have investigated the macromolecules that contribute to the brain 1H NMR spectrum. The cerebral cortex showed distinct resonances at the uncrowded methyl- and methylene chemical shift scale of the spin-echo 1H NMR spectrum. The peaks at 1.22 and 1.40 ppm (relative to the methyl protons of N-acetyl aspartate at 2.02 ppm) arise from cerebral macromolecules without evidence for co-resonances from low molecular weight metabolites as shown by the spin-spin relaxation decays of these resonances. In addition to these NMR signals, peaks at 0.9 and 1.7 ppm from macromolecules were detected. These resonances are from proteins, and we have identified the polypeptides that contributed to the 1H NMR peaks. Two proteins that were present at concentrations of 250 and 350 micrograms/g of dryed tissue showed 1H NMR spectra that resembled the macromolecular pattern in the cerebral 1H NMR spectrum. They were identified as thymosin beta 4 and histone H1, respectively. Thymosin beta 4 was present in soluble high speed cytoplasmic fraction and in P2 pellet, whereas histone H1 was detected in nuclear enriched fraction. A chemical shift-correlated two-dimensional 1H NMR spectrum of thymosin beta 4 in vitro revealed a coupling pattern that matched the macromolecule in the cerebral cortex which we have previously noted (Kauppinen R. A., Kokko, H., and Williams, S. R. (1992) J. Neurochem. 58, 967-974). On the basis of both one- and two-dimensional NMR evidence, subcellular distribution and high concentration, we assign the 1H NMR signals at 0.9, 1.22, 1.40, and 1.7 ppm in the cerebral cortex to thymosin beta 4.

Knowledge & Management of Aquatic Ecosystems, 2020

The narrow-clawed crayfish (Pontastacus leptodactylus) is an alien species in Finland with only a... more The narrow-clawed crayfish (Pontastacus leptodactylus) is an alien species in Finland with only a few populations reported from the southeastern region during the last century. We discovered a productive population in the lake Jängynjärvi, which is upstream from the previously reported wild narrow-clawed crayfish population in that region. Preliminary studies indicated that this population is not infected with Aphanomyces astaci. We collected narrow-clawed crayfish samples from the lake Jängynjärvi population for both infection challenge and genetic studies, in order to investigate possible A. astaci resistance among this Finnish population and to evaluate their phylogenetic position that would enable us to speculate different scenarios of distribution pathways or origin of the population. The infection studies indicated that the narrow-clawed crayfish in this population were more resistant against A. astaci infection (B haplogroup A. astaci) compared to the noble crayfish (Astacus ...

Phytopathology Research, 2020

Phytophthora fragariae causes drastic damage in strawberry crops. P. fragariae infects strawberry... more Phytophthora fragariae causes drastic damage in strawberry crops. P. fragariae infects strawberry roots and causes red stele root rot. Although P. fragariae is a quarantine organism, its spread in Finland continues as more and more fields contract the disease. The spread can be halted through developing rapid and reliable detection assays. We have developed a rapid recombinase polymerase amplification (RPA) assay for P. fragariae targeting the Phytophthora mitochondrial DNA intergenic atp9-nad9 marker. The assay is DNA-extraction free and capable of detecting as low as 10 fg of P. fragariae genomic DNA. We found the assay reliable for diagnosing field plants when samples are adequately collected. We also applied the RPA assay to the detection of the pathogen in the soil through coupling the assay with baiting with the host plant. The results suggest that if only a small number of samples are analysed, the baiting results will not be reliable.

Botany, 2018

Fluctuations in the yield of wild berries are markedly influenced by weather conditions. However,... more Fluctuations in the yield of wild berries are markedly influenced by weather conditions. However, the cause–effect relationship is often poorly understood. Based on data spanning a 20-year period in Finland, we made an effort to elucidate the influence of different weather conditions on the yield of arctic bramble (Rubus arcticus L.). We analyzed the regression coefficients of various weather conditions in several regression models using the elaboration approach. Temperature accumulated in July had a positive effect on yield. Yield was negatively influenced by temperature accumulated during the previous summer, rainfall in the October of the previous year, and temperature accumulated in May of the same year. It is notable that the same weather conditions had a positive influence on yield of the same year whereas these conditions had a negative effect on the yield potential of the following year. Compared with traditional analysis methods, the elaboration approach provided a better u...

Knowledge & Management of Aquatic Ecosystems, 2018

We studied the presence of possible Aphanomyces astaci infections in eight Turkish narrow-clawed ... more We studied the presence of possible Aphanomyces astaci infections in eight Turkish narrow-clawed crayfish (Astacus leptodactylus) populations by analyzing the prevalence and genotypes of the disease agent A. astaci. The qPCR analyses revealed A. astaci infection in seven of the studied eight populations, with the agent level A2 or higher. The agent levels among the infected populations varied from A0 to A5, i.e., from negative to high level of infection, based on qPCR ranking. Based on the sequencing of the chitinase gene and the mitochondrial ribosomal rnnS and rnnL subunits, we detected both A (As) and B (PsI) haplogroups of A. astaci in our samples, with each of the studied populations being carriers of only one haplotype. The results confirm previous detections of A. astaci in Turkish narrow-clawed crayfish populations and reveal, that both A and B haplogroup A. astaci carriers exist widely in A. leptodactylus populations of Turkey.

Knowledge and Management of Aquatic Ecosystems, 2014

The carrier status and possible elevated tolerance of the signal crayfish (Pacifastacus leniuscul... more The carrier status and possible elevated tolerance of the signal crayfish (Pacifastacus leniusculus) against the crayfish plague disease agent (Aphanomyces astaci) has been speculated for several decades. We studied experimentally the responses of the signal crayfish from two Finnish populations against the crayfish plague infection by using two crayfish plague isolates with differing virulences; the highly virulent PsI-isolate and the mid virulent As-isolate. The studied signal crayfish came from two origins: the wild Leppävirta population and the Raukola farmed population of mixed genetic background. Both test groups were infected with A. astaci isolates using the challenge of 10 000 spores mL −1. The isolates were PsI-Puujärvi (UEF8866-2) from Lake Puujärvi signal crayfish (year 2003) and As-Kivesjärvi (Evira6462/06) from Lake Kivesjärvi noble crayfish (year 2005 epidemic) in Finland. The crayfish were sampled prior to the experimental challenge with A. astaci to evaluate their A. astaci carrier status. The mortality, molting, feeding activity and other behavior of the crayfish were followed during the experiment. We observed increased mortality of the infected groups, related to the molting in some cases, and delayed molting. The impacts of the intense crayfish plague infection on the signal crayfish were clear and the studied populations showed differences in their reactions that are potentially explained by differing physiological conditions and different molt cycle phase. The results show that infection of both tested crayfish plague genotypes affects signal crayfish and is likely one of the main reasons behind losses among signal crayfish populations. RÉSUMÉ L'écrevisse signal est vulnérable aux deux génotypes As et PsI de la peste de l'écrevisse

Acta Horticulturae, 2017

Oomycete species belonging to Phytophthora and Pythium genera can cause root, crown or fruit rots... more Oomycete species belonging to Phytophthora and Pythium genera can cause root, crown or fruit rots of strawberry. In this study, we have isolated and identified by sequencing twelve novel oomycete isolates from strawberry plantations showing disease symptoms or weak growth. Virulences of four new Phytophthora and two Pythium isolates were tested using detached leaflets of four strawberry cultivars ('Bounty', 'Honeoye', 'Jonsok', 'Polka') and also with runners and roots of 'Polka'. Two of the Phytophthora isolates (GE5 and SO18) showed very low virulence, whereas Phytophthora cactorum isolate Pc407, used as a positive control, was the most aggressive towards leaflets and runners. It caused significant necrotic lesions in all cultivars but 'Bounty', which is known to be quite resistant against crown rot. The most sensitive cultivar was 'Polka'. P. megasperma isolates (SO6 and GE9) and two Pythium isolates (LG1 and SO28) represented intermediate virulence in the runners of 'Polka', but in the leaflets lesions were quite small compared to Pc407. In contrast, LG1, SO28 and SO6 rapidly induced lesions in the detached roots, suggesting that they may be more virulent towards roots than leaf tissues. The ability of these isolates to cause root rot and stunting symptoms on strawberry should be further studied using whole plants.

MycoKeys, 2016

Microbial metabarcoding studies using high throughput sequencing technologies generate unpreceden... more Microbial metabarcoding studies using high throughput sequencing technologies generate unprecedented amounts of DNA sequence data and make it possible to determine not only the composition of the communities but also the underlying factors powering the evolution of these communities. Despite the potential of community level studies in helping to better understand the ecology of pathogens and to manage the losses caused by them, very few oomycete addressing metabarcoding studies have been carried out and with highly variable results. The aim of this study was to develop new oomycete-specific ITS region PCR primers with improved specificity for metabarcoding and identification of oomycetes. The modified ITS1oo and the newly developed ITS3oo primers show improved in silico specificity for oomycetes and when paired with the universal ITS4 successfully amplified the DNA from all eleven tested oomycete species from six genera. High throughput sequencing of 20 soil samples from forest nurseries and bordering areas, using the primer pair ITS1oo/ITS4, recovered more than 400 oomycete OTUs, which is a significant increase over previous studies, and indicates the ability of the new method to detect various oomycete groups from complex substrates. The average fraction of oomycete reads per soil samples was 32-36%, with a maximum of 69%. The recovered oomycete OTUs represented the groups Lagenidiales, Peronosporales, Pythiales and Saprolegniales, with Pythiales dominating in all samples. In addition, the new primers were successfully used in identifying pathogens directly from infected plant tissues with Sanger sequencing. The pathogen was identified to the species or genus level in four samples out of six. In conclusion, the developed oomycete-specific primers provide a reliable method for the identification and metabarcoding of oomycetes.

DOAJ (DOAJ: Directory of Open Access Journals), Mar 1, 2022

Acta Agriculturae Scandinavica Section B-soil and Plant Science, Nov 1, 2022

IV International Strawberry Symposium, 2002

Plant-derived flavonoid compounds act as protective nutrients possessing antioxidant and free rad... more Plant-derived flavonoid compounds act as protective nutrients possessing antioxidant and free radical scavenging activity in foods. An HPLC-based quantitative procedure with improved extraction and hydrolysis was used to analyse the content of the flavonols myricetin, quercetin and kaempferol in strawberry cultivars. The quercetin contents in strawberry cultivars ranged from 0.7 to 2.6 mg 100 g-1 fresh weight. The kaempferol levels ranged from 0.9 to 2.2 mg 100 g-1. In cv. Senga Sengana the amount of myricetin was hardly detectable, while in cv. Honeoye it was 1.7 mg 100 g-1. The sum of the three flavonols varied greatly among the strawberry cultivars. In general, cv. Honeoye (fairly resistant to fungal diseases) contained the highest amount of flavonols and the old cv. Senga Sengana (susceptible to fungal diseases) contained the lowest amount of flavonols. The high variability in the flavonol contents offers possible avenues for identifying and selecting strawberry genotypes rich in health-promoting compounds.

Freshwater crayfish, Apr 15, 2021

Eroded swimmeret syndrome (ESS) was first described in 2014 from Swedish signal crayfish (Pacifas... more Eroded swimmeret syndrome (ESS) was first described in 2014 from Swedish signal crayfish (Pacifastacus leniusculus (Dana)), and later also from Finland, with gross symptoms and disease agent candidates identified and described by 2015. The ESS was first discovered affecting alien signal crayfish in Fennoscandia. The ESS is caused by a multiple infection involving Aphanomyces astaci (Schikora) and Fusarium species complex (SC). The ESS symptoms include first melanised spots in swimmerets, then partial swimmeret erosion and finally loss of a swimmeret. There could be a total loss of all swimmerets in the most severe cases. Both females and males can be affected by the ESS. In females, the ESS lowers reproductive success while in males the ESS often causes erosion of the gonopods and thus possible partial failure in mating. The ESS is more frequent among mature females that have reproduced once compared to immature females or those that are mature but have not yet reproduced. The proportion of females with ESS has ranged from 10 to 50% among Lake Saimaa signal crayfish in Finland and in a wider survey from Sweden the range was from 0 to 38%. Among Lake Saimaa male signal crayfish, the ESS proportion has been less than 10%, while it was only 0.6% in the Swedish data. The ESS has also been observed among alien signal crayfish in Switzerland. There are recent observations of ESS affecting narrow-clawed crayfish, Pontastacus leptodactylus (Eschscholtz), in Croatia and Romania (i.e., among native European crayfish stocks). Here, we summarise current knowledge about the ESS and speculate on a few potentially crucial impacts of this syndrome.

Phytopathology®, 2018

The phytopathogen Phytophthora cactorum infects economically important herbaceous and woody plant... more The phytopathogen Phytophthora cactorum infects economically important herbaceous and woody plant species. P. cactorum isolates differ in host specificity; for example, strawberry crown rot is often caused by a specialized pathotype. Here we compared the transcriptomes of two P. cactorum isolates that differ in their virulence to garden strawberry (Pc407: high virulence; Pc440: low virulence). De novo transcriptome assembly and clustering of contigs resulted in 19,372 gene clusters. Two days after inoculation of Fragaria vesca roots, 3,995 genes were differently expressed between the P. cactorum isolates. One of the genes that were highly expressed only in Pc407 encodes a GAF sensor protein potentially involved in membrane trafficking processes. Two days after inoculation, elicitins were highly expressed in Pc407 and lipid catabolism appeared to be more active than in Pc440. Of the carbohydrate-active enzymes, those that degrade pectin were often more highly expressed in Pc440, wher...

Neurochemistry International, 1992

Additional file 1 Figure S1. Screenshots of Geneious alignment for the atp9-nad9 sequences of Phy... more Additional file 1 Figure S1. Screenshots of Geneious alignment for the atp9-nad9 sequences of Phytophthora species provided by Miles et al. (2015). For the P. fragariae atp9-nad9 sequence, primers and probe binding regions are annotated.

Journal of Biological Chemistry, 1992

In the present work we have investigated the macromolecules that contribute to the brain 1H NMR s... more In the present work we have investigated the macromolecules that contribute to the brain 1H NMR spectrum. The cerebral cortex showed distinct resonances at the uncrowded methyl- and methylene chemical shift scale of the spin-echo 1H NMR spectrum. The peaks at 1.22 and 1.40 ppm (relative to the methyl protons of N-acetyl aspartate at 2.02 ppm) arise from cerebral macromolecules without evidence for co-resonances from low molecular weight metabolites as shown by the spin-spin relaxation decays of these resonances. In addition to these NMR signals, peaks at 0.9 and 1.7 ppm from macromolecules were detected. These resonances are from proteins, and we have identified the polypeptides that contributed to the 1H NMR peaks. Two proteins that were present at concentrations of 250 and 350 micrograms/g of dryed tissue showed 1H NMR spectra that resembled the macromolecular pattern in the cerebral 1H NMR spectrum. They were identified as thymosin beta 4 and histone H1, respectively. Thymosin beta 4 was present in soluble high speed cytoplasmic fraction and in P2 pellet, whereas histone H1 was detected in nuclear enriched fraction. A chemical shift-correlated two-dimensional 1H NMR spectrum of thymosin beta 4 in vitro revealed a coupling pattern that matched the macromolecule in the cerebral cortex which we have previously noted (Kauppinen R. A., Kokko, H., and Williams, S. R. (1992) J. Neurochem. 58, 967-974). On the basis of both one- and two-dimensional NMR evidence, subcellular distribution and high concentration, we assign the 1H NMR signals at 0.9, 1.22, 1.40, and 1.7 ppm in the cerebral cortex to thymosin beta 4.

Knowledge & Management of Aquatic Ecosystems, 2020

The narrow-clawed crayfish (Pontastacus leptodactylus) is an alien species in Finland with only a... more The narrow-clawed crayfish (Pontastacus leptodactylus) is an alien species in Finland with only a few populations reported from the southeastern region during the last century. We discovered a productive population in the lake Jängynjärvi, which is upstream from the previously reported wild narrow-clawed crayfish population in that region. Preliminary studies indicated that this population is not infected with Aphanomyces astaci. We collected narrow-clawed crayfish samples from the lake Jängynjärvi population for both infection challenge and genetic studies, in order to investigate possible A. astaci resistance among this Finnish population and to evaluate their phylogenetic position that would enable us to speculate different scenarios of distribution pathways or origin of the population. The infection studies indicated that the narrow-clawed crayfish in this population were more resistant against A. astaci infection (B haplogroup A. astaci) compared to the noble crayfish (Astacus ...

Phytopathology Research, 2020

Phytophthora fragariae causes drastic damage in strawberry crops. P. fragariae infects strawberry... more Phytophthora fragariae causes drastic damage in strawberry crops. P. fragariae infects strawberry roots and causes red stele root rot. Although P. fragariae is a quarantine organism, its spread in Finland continues as more and more fields contract the disease. The spread can be halted through developing rapid and reliable detection assays. We have developed a rapid recombinase polymerase amplification (RPA) assay for P. fragariae targeting the Phytophthora mitochondrial DNA intergenic atp9-nad9 marker. The assay is DNA-extraction free and capable of detecting as low as 10 fg of P. fragariae genomic DNA. We found the assay reliable for diagnosing field plants when samples are adequately collected. We also applied the RPA assay to the detection of the pathogen in the soil through coupling the assay with baiting with the host plant. The results suggest that if only a small number of samples are analysed, the baiting results will not be reliable.

Botany, 2018

Fluctuations in the yield of wild berries are markedly influenced by weather conditions. However,... more Fluctuations in the yield of wild berries are markedly influenced by weather conditions. However, the cause–effect relationship is often poorly understood. Based on data spanning a 20-year period in Finland, we made an effort to elucidate the influence of different weather conditions on the yield of arctic bramble (Rubus arcticus L.). We analyzed the regression coefficients of various weather conditions in several regression models using the elaboration approach. Temperature accumulated in July had a positive effect on yield. Yield was negatively influenced by temperature accumulated during the previous summer, rainfall in the October of the previous year, and temperature accumulated in May of the same year. It is notable that the same weather conditions had a positive influence on yield of the same year whereas these conditions had a negative effect on the yield potential of the following year. Compared with traditional analysis methods, the elaboration approach provided a better u...

Knowledge & Management of Aquatic Ecosystems, 2018

We studied the presence of possible Aphanomyces astaci infections in eight Turkish narrow-clawed ... more We studied the presence of possible Aphanomyces astaci infections in eight Turkish narrow-clawed crayfish (Astacus leptodactylus) populations by analyzing the prevalence and genotypes of the disease agent A. astaci. The qPCR analyses revealed A. astaci infection in seven of the studied eight populations, with the agent level A2 or higher. The agent levels among the infected populations varied from A0 to A5, i.e., from negative to high level of infection, based on qPCR ranking. Based on the sequencing of the chitinase gene and the mitochondrial ribosomal rnnS and rnnL subunits, we detected both A (As) and B (PsI) haplogroups of A. astaci in our samples, with each of the studied populations being carriers of only one haplotype. The results confirm previous detections of A. astaci in Turkish narrow-clawed crayfish populations and reveal, that both A and B haplogroup A. astaci carriers exist widely in A. leptodactylus populations of Turkey.

Knowledge and Management of Aquatic Ecosystems, 2014

The carrier status and possible elevated tolerance of the signal crayfish (Pacifastacus leniuscul... more The carrier status and possible elevated tolerance of the signal crayfish (Pacifastacus leniusculus) against the crayfish plague disease agent (Aphanomyces astaci) has been speculated for several decades. We studied experimentally the responses of the signal crayfish from two Finnish populations against the crayfish plague infection by using two crayfish plague isolates with differing virulences; the highly virulent PsI-isolate and the mid virulent As-isolate. The studied signal crayfish came from two origins: the wild Leppävirta population and the Raukola farmed population of mixed genetic background. Both test groups were infected with A. astaci isolates using the challenge of 10 000 spores mL −1. The isolates were PsI-Puujärvi (UEF8866-2) from Lake Puujärvi signal crayfish (year 2003) and As-Kivesjärvi (Evira6462/06) from Lake Kivesjärvi noble crayfish (year 2005 epidemic) in Finland. The crayfish were sampled prior to the experimental challenge with A. astaci to evaluate their A. astaci carrier status. The mortality, molting, feeding activity and other behavior of the crayfish were followed during the experiment. We observed increased mortality of the infected groups, related to the molting in some cases, and delayed molting. The impacts of the intense crayfish plague infection on the signal crayfish were clear and the studied populations showed differences in their reactions that are potentially explained by differing physiological conditions and different molt cycle phase. The results show that infection of both tested crayfish plague genotypes affects signal crayfish and is likely one of the main reasons behind losses among signal crayfish populations. RÉSUMÉ L'écrevisse signal est vulnérable aux deux génotypes As et PsI de la peste de l'écrevisse

Acta Horticulturae, 2017

Oomycete species belonging to Phytophthora and Pythium genera can cause root, crown or fruit rots... more Oomycete species belonging to Phytophthora and Pythium genera can cause root, crown or fruit rots of strawberry. In this study, we have isolated and identified by sequencing twelve novel oomycete isolates from strawberry plantations showing disease symptoms or weak growth. Virulences of four new Phytophthora and two Pythium isolates were tested using detached leaflets of four strawberry cultivars ('Bounty', 'Honeoye', 'Jonsok', 'Polka') and also with runners and roots of 'Polka'. Two of the Phytophthora isolates (GE5 and SO18) showed very low virulence, whereas Phytophthora cactorum isolate Pc407, used as a positive control, was the most aggressive towards leaflets and runners. It caused significant necrotic lesions in all cultivars but 'Bounty', which is known to be quite resistant against crown rot. The most sensitive cultivar was 'Polka'. P. megasperma isolates (SO6 and GE9) and two Pythium isolates (LG1 and SO28) represented intermediate virulence in the runners of 'Polka', but in the leaflets lesions were quite small compared to Pc407. In contrast, LG1, SO28 and SO6 rapidly induced lesions in the detached roots, suggesting that they may be more virulent towards roots than leaf tissues. The ability of these isolates to cause root rot and stunting symptoms on strawberry should be further studied using whole plants.

MycoKeys, 2016

Microbial metabarcoding studies using high throughput sequencing technologies generate unpreceden... more Microbial metabarcoding studies using high throughput sequencing technologies generate unprecedented amounts of DNA sequence data and make it possible to determine not only the composition of the communities but also the underlying factors powering the evolution of these communities. Despite the potential of community level studies in helping to better understand the ecology of pathogens and to manage the losses caused by them, very few oomycete addressing metabarcoding studies have been carried out and with highly variable results. The aim of this study was to develop new oomycete-specific ITS region PCR primers with improved specificity for metabarcoding and identification of oomycetes. The modified ITS1oo and the newly developed ITS3oo primers show improved in silico specificity for oomycetes and when paired with the universal ITS4 successfully amplified the DNA from all eleven tested oomycete species from six genera. High throughput sequencing of 20 soil samples from forest nurseries and bordering areas, using the primer pair ITS1oo/ITS4, recovered more than 400 oomycete OTUs, which is a significant increase over previous studies, and indicates the ability of the new method to detect various oomycete groups from complex substrates. The average fraction of oomycete reads per soil samples was 32-36%, with a maximum of 69%. The recovered oomycete OTUs represented the groups Lagenidiales, Peronosporales, Pythiales and Saprolegniales, with Pythiales dominating in all samples. In addition, the new primers were successfully used in identifying pathogens directly from infected plant tissues with Sanger sequencing. The pathogen was identified to the species or genus level in four samples out of six. In conclusion, the developed oomycete-specific primers provide a reliable method for the identification and metabarcoding of oomycetes.