scholarly journals The Diplodia Tip Blight Pathogen Sphaeropsis sapinea is the Most Common Fungus in Scots Pines’ Mycobiome, Irrespective of Health Status—A Case Study from Germany

2021 ◽  
Vol 7 (8) ◽  
pp. 607
Author(s):  
Kathrin Blumenstein ◽  
Johanna Bußkamp ◽  
Gitta Jutta Langer ◽  
Ewald Johannes Langer ◽  
Eeva Terhonen
Keyword(s):  
Health Status ◽  
High Throughput Sequencing ◽  
Disease Outbreaks ◽  
Opportunistic Pathogen ◽  
Its2 Region ◽  
Disease Symptoms ◽  
Age Related ◽  
Sphaeropsis Sapinea ◽  
Coniferous Tree Species

The opportunistic pathogen Sphaeropsis sapinea (≡ Diplodia sapinea) is one of the most severe pathogens in Scots pine, causing the disease Diplodia tip blight on coniferous tree species. Disease symptoms become visible when trees are weakened by stress. Sphaeropsis sapinea has an endophytic mode in its lifecycle, making it difficult to detect before disease outbreaks. This study aims to record how S. sapinea accumulates in trees of different health status and, simultaneously, monitor seasonal and age-related fluctuations in the mycobiome. We compared the mycobiome of healthy and diseased Scots pines. Twigs were sampled in June and September 2018, and filamentous fungi were isolated. The mycobiome was analyzed by high-throughput sequencing (HTS) of the ITS2 region. A PERMANOVA analysis confirmed that the mycobiome community composition significantly differed between growth years (p < 0.001) and sampling time (p < 0.001) but not between healthy and diseased trees. Sphaeropsis sapinea was the most common endophyte isolated and the second most common in the HTS data. The fungus was highly abundant in symptomless (healthy) trees, presenting in its endophytic mode. Our results highlight the ability of S. sapinea to accumulate unnoticed as an endophyte in healthy trees before the disease breaks out, representing a sudden threat to Scots pines in the future, especially with increasing drought conditions experienced by pines.

scholarly journals The Opportunistic Pathogen Sphaeropsis Sapinea is Found to be one of the Most Abundant Fungi in Symptomless and Diseased Scots Pine in Central-Europe

2020 ◽  
Author(s):  
Kathrin Blumenstein ◽  
Gitta Langer ◽  
Johanna Bußkamp ◽  
Ewald Langer ◽  
Eeva Terhonen
Keyword(s):  
Internal Transcribed Spacer ◽  
High Throughput Sequencing ◽  
Fungal Endophytes ◽  
Disease Outbreaks ◽  
Opportunistic Pathogen ◽  
Forest Stand ◽  
Sampling Time ◽  
Its2 Region ◽  
Disease Symptoms ◽  
Sphaeropsis Sapinea

Abstract Background: The opportunistic and latent pathogen Sphaeropsis sapinea is one of the most important forest pathogens on pine. The fungus may cause Diplodia tip blight on several coniferous trees and disease symptoms come visible when trees are weakened by stress, usually related to injuries and drought. This project compares the mycobiome of healthy and diseased Scots pines. Twigs were sampled in June and September 2018 in a German forest stand with varying health status of the sampled Scots pines. Growth of 2017 and 2018 were sampled and cultivable, filamentous fungi isolated and the mycobiome was analysed by high-throughput sequencing (HTS) of the internal transcribed spacer 2 (ITS2) region. Results: A PERMANOVA analysis confirmed that the mycobiome community composition significantly differed between growth years (p < 0.001) and sampling time (p < 0.001) but not between healthy and diseased trees. Higher amount of S. sapinea was observed in June and the growth year 2017. Besides yeasts which were neglected, 23 ascomyceteous fungal endophytes were isolated. S. sapinea was the most common endophyte isolated and the second common in HTS data. It was highly abundant in symptomless (healthy) trees. Conclusion: Results highlights the ability of S. sapinea to accumulate unnoticed before disease outbreaks, implementing the sudden threat for Scots pines in the future.

scholarly journals Fungal Diversity in the Phyllosphere of Pinus heldreichii H. Christ—An Endemic and High-Altitude Pine of the Mediterranean Region

Diversity ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 172 ◽  
Author(s):  
Jelena Lazarević ◽  
Audrius Menkis
Keyword(s):  
High Altitude ◽  
Bark Beetles ◽  
Fungal Pathogens ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
High Quality ◽  
The Balkans ◽  
Fungal Community Structure ◽  
Growing Conditions ◽  
Coniferous Tree Species

Pinus heldreichii is a high-altitude coniferous tree species naturaly occurring in small and disjuncted populations in the Balkans and southern Italy. The aim of this study was to assess diversity and composition of fungal communities in living needles of P. heldreichii specifically focusing on fungal pathogens. Sampling was carried out at six different sites in Montenegro, where 2-4 year-old living needles of P. heldreichii were collected. Following DNA isolation, it was amplified using ITS2 rDNA as a marker and subjected to high-throughput sequencing. Sequencing resulted in 31,831 high quality reads, which after assembly were found to represent 375 fungal taxa. The detected fungi were 295 (78.7%) Ascomycota, 79 (21.0%) Basidiomycota and 1 (0.2%) Mortierellomycotina. The most common fungi were Lophodermium pinastri (12.5% of all high-quality sequences), L. conigenum (10.9%), Sydowia polyspora (8.8%), Cyclaneusma niveum (5.5%), Unidentified sp. 2814_1 (5.4%) and Phaeosphaeria punctiformis (4.4%). The community composition varied among different sites, but in this respect two sites at higher altitudes (harsh growing conditions) were separated from three sites at lower altitudes (milder growing conditions), suggesting that environmental conditions were among major determinants of fungal communities associated with needles of P. heldreichii. Trees on one study site were attacked by bark beetles, leading to discolouration and frequent dieback of needles, thereby strongly affecting the fungal community structure. Among all functional groups of fungi, pathogens appeared to be an important component of fungal communities in the phyllosphere of P. heldreichii, especially in those trees under strong abiotic and biotic stress.

scholarly journals Modelling the Evolutionary Dynamics of Viruses within Their Hosts: A Case Study Using High-Throughput Sequencing

2012 ◽  
Vol 8 (4) ◽  
pp. e1002654 ◽  
Author(s):  
Frédéric Fabre ◽  
Josselin Montarry ◽  
Jérôme Coville ◽  
Rachid Senoussi ◽  
Vincent Simon ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Evolutionary Dynamics

scholarly journals Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity

2017 ◽  
Vol 83 (17) ◽  
Author(s):  
Francesca De Filippis ◽  
Manolo Laiola ◽  
Giuseppe Blaiotta ◽  
Danilo Ercolini
Keyword(s):  
Microbial Ecology ◽  
High Throughput ◽  
Biological Samples ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Fungal Communities ◽  
Its2 Region ◽  
Mock Community

ABSTRACT Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes, with 16S rRNA being the gold standard for bacteria. As for fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity. After an in silico primer evaluation, we compared three amplicons (the ITS1-ITS2 region [ITS1-2], 18S ribosomal small subunit RNA, and the D1/D2 domain of the 26S ribosomal large subunit RNA), using biological samples and a mock community of common fungal species. All three targets allowed for accurate identification of the species present. Nevertheless, high heterogeneity in ITS1-2 length was found, and this caused an overestimation of the abundance of species with a shorter ITS, while both 18S and 26S amplicons allowed for more reliable quantification. We demonstrated that ITS1-2 amplicon sequencing, although widely used, may lead to an incorrect evaluation of fungal communities, and efforts should be made to promote the use of different targets in sequencing-based microbial ecology studies. IMPORTANCE Amplicon-sequencing approaches for fungi may rely on different targets affecting the diversity and abundance of the fungal species. An increasing number of studies will address fungal diversity by high-throughput amplicon sequencing. The description of the communities must be accurate and reliable in order to draw useful insights and to address both ecological and biological questions. By analyzing a mock community and several biological samples, we demonstrate that using different amplicon targets may change the results of fungal microbiota analysis, and we highlight how a careful choice of the target is fundamental for a thorough description of the fungal communities.

scholarly journals Exploring and Expanding the Category of ‘Young Workers’ According to Situated Ways of Doing Risk and Safety—a Case Study in the Retail Industry

2013 ◽  
Vol 3 (3) ◽  
pp. 219 ◽  
Author(s):  
Mette Lykke Nielsen ◽  
Johnny Dyreborg ◽  
Pete Kines ◽  
Kent J. Nielsen ◽  
Kurt Rasmussen
Keyword(s):  
Young Adult ◽  
Individual Characteristics ◽  
Skilled Workers ◽  
School Dropouts ◽  
Cognitive Limitations ◽  
Age Related ◽  
Group Interviews ◽  
Student Workers ◽  
Retail Workers

Young adult workers aged 18–24 years have the highest risk of accidents at work. Following the work of Bourdieu and Tannock, we demonstrate that young adult workers are a highly differentiated group. Accordingly, safety prevention among young adult workers needs to be nuanced in ways that take into consideration the different positions and conditions under which young adult workers are employed. Based on single and group interviews with 26 young adult workers from six various sized supermarkets, we categorize young adult retail workers into the following five distinct groups: ‘Skilled workers,’ ‘Apprentices,’ ‘Sabbatical year workers,’ ‘Student workers,’ and ‘School dropouts.’ We argue that exposure to accidental risk is not equally distributed among them and offer an insight into the narratives of young adult workers on the subject of risk situations at work. The categorizations are explored and expanded according to the situated ways of ‘doing’ risk and safety in the working practices of the adult workers. We suggest that the understanding of ‘young’ as an age-related biological category might explain why approaches to prevent accidents among young employees first and foremost include individual factors like advice, information, and supervision and to a lesser degree the structural and cultural environment wherein they are embedded. We conclude that age cannot stand alone as the only factor in safety prevention directed at workers aged 18–24 years; if we do so, there is a risk of overemphasizing age-related individual characteristics such as awareness and cognitive limitations before structural, relational, and hierarchical dimensions at the workplace.

scholarly journals High-Throughput Sequencing Identifies Novel Viruses in Nectarine: Insights to the Etiology of Stem-Pitting Disease

2016 ◽  
Vol 106 (5) ◽  
pp. 519-527 ◽  
Author(s):  
D. E. V. Villamor ◽  
T. A. Mekuria ◽  
S. S. Pillai ◽  
K. C. Eastwell
Keyword(s):  
High Throughput ◽  
Pathogen Detection ◽  
High Throughput Sequencing ◽  
Prunus Persica ◽  
Disease Symptoms ◽  
Testing Procedures ◽  
Molecular Tests ◽  
Putative Member ◽  
Stem Pitting ◽  
Virus Testing

Recent studies have shown the superiority of high-throughput sequencing (HTS) technology over many standard protocols for pathogen detection. HTS was initiated on fruit tree accessions from disparate sources to improve and advance virus-testing procedures. A virus with genomic features resembling most closely that of the recently described Nectarine stem-pitting-associated virus, putative member of genus Luteovirus, was found in three nectarine trees (Prunus persica cv. nectarina), each exhibiting stem-pitting symptoms on the woody cylinder above the graft union. In these samples, HTS also revealed the presence of a coinfecting virus with genome characteristics typical of members of the genus Marafivirus. The same marafivirus- and luteovirus-like viruses were detected in nonsymptomatic nectarine and peach selections, indicating only a loose relationship between these two viruses with nectarine stem-pitting disease symptoms. Two selections infected with each of these viruses had previously tested free of known virus or virus-like agents using the current biological, serological, and molecular tests employed at the Clean Plant Center Northwest. Overall, this study presents the characterization by HTS of novel marafivirus- and luteovirus-like viruses of nectarine, and provides further insights into the etiology of nectarine stem-pitting disease. The discovery of these new viruses emphasizes the ability of HTS to reveal viruses that are not detected by existing protocols.

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