scholarly journals Cryptic Risks to Forest Biosecurity Associated with the Global Movement of Commercial Seed

Forests ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 459 ◽  
Author(s):  
Michelle Cleary ◽  
Funda Oskay ◽  
Hatice Tugba Doğmuş ◽  
Asko Lehtijärvi ◽  
Stephen Woodward ◽  
...  
Keyword(s):  
Potential Risk ◽  
Tree Species ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Plant Protection ◽  
Forest Tree ◽  
Operational Taxonomic Units ◽  
Pinus Species ◽  
Seed Health ◽  
Global Movement

The import and export of tree seed carries with it risks of inadvertent introduction of pests and pathogens to hitherto unaffected regions. Although trade in seed of specified trees is regulated, phytosanitary requirements for most tree species are minimal, even those related to the most important forest tree species in a given region. A better understanding of the microbiome associated with seed intended for commercial production or ornamental use, and their potential risk with the transport from the source origin of distributors, will help regulatory agencies implement measures to safeguard seed health and avoid trade-related spread of potentially harmful pathogens. In this study we used high-throughput sequencing to show that highly diverse fungal communities were associated with seed of 14 different Pinus species obtained from seed banks (seed orchards) and retail sources (online distributors) in North America and Europe. Fungal diversity differed among the 23 seedlots tested. Community composition did not relate to the species of Pinus nor the country of origin. Assigned potential functions based on sequence identity using FUNGuild provided an overall understanding of the likely life strategies of fungal operational taxonomic units (OTUs). Of those sequences classified to a trophic level, 453 were plant pathogens, with the Dothideomycetes having the highest prevalence. The most common plant pathogens included Sydowia polyspora, Lasiodiplodia theobromae, Diplodia intermedia and Diplodia sapinea that were detected from the majority of Pinus species. The evidence presented here illustrates an urgent need for plant protection authorities, practitioners and the general public to recognize the potential risk of introducing harmful pathogens through innocent transport of seed.

scholarly journals Cryptic Risks to Forest Biosecurity Associated with the Global Movement of Commercial Seed

2019 ◽  
Author(s):  
Michelle Cleary ◽  
Funda Oskay ◽  
Hatice Tugba Doğmuş ◽  
Asko Lehtijärvi ◽  
Stephen Woodward ◽  
...  
Keyword(s):  
Potential Risk ◽  
Tree Species ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Plant Protection ◽  
Forest Tree ◽  
Regulatory Agencies ◽  
Global Movement ◽  
Import And Export ◽  
Common Plant

The import and export of tree seed carries with it risks of inadvertent introduction of pests and pathogens to hitherto unaffected regions. Although trade in seed of specified trees is regulated, phytosanitary requirements for most tree species are minimal, even those related to the most important forest tree species in a given region. A better understanding of the microbiome associated with seed intended for commercial production or ornamental use, and their potential risk with the transport from the source origin of distributors, will help regulatory agencies implement measures to prevent new and emerging risks. In this study we used high throughput sequencing to show that highly diverse fungal communities were associated with seed of 14 different Pinus species obtained from seed banks (seed orchards) and retail sources (online distributors) in North America and Europe. Fungal diversity differed among the 23 seedlots tested. Community composition did not relate to the species of Pinus nor the country of origin. Assigned potential functions based on sequence identity using FUNGuild provided an overall understanding of the likely life strategies associated fungal OTUs. Of those sequences classified to a trophic level, 453 were plant pathogens, with the Dothideomycetes having the highest prevalence. The most common plant pathogens detected included Sydowia polyspora, Lasiodiplodia theobromae, Diplodia intermedia and Diplodia sapinea. The evidence presented here illustrates an urgent need for plant protection authorities, practitioners and the general public to recognize the potential risk of introducing harmful pathogens through innocent transport of seed.

scholarly journals Genus-Specific Primers for Study of Fusarium Communities in Field Samples

2015 ◽  
Vol 82 (2) ◽  
pp. 491-501 ◽  
Author(s):  
Ida Karlsson ◽  
Véronique Edel-Hermann ◽  
Nadine Gautheron ◽  
Mikael Brandström Durling ◽  
Anna-Karin Kolseth ◽  
...  
Keyword(s):  
High Throughput ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Elongation Factor ◽  
Specific Primers ◽  
Translation Elongation ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Field Samples ◽  
High Discriminatory Power

ABSTRACTFusariumis a large and diverse genus of fungi of great agricultural and economic importance, containing many plant pathogens and mycotoxin producers. To date, high-throughput sequencing ofFusariumcommunities has been limited by the lack of genus-specific primers targeting regions with high discriminatory power at the species level. In the present study, we evaluated twoFusarium-specific primer pairs targeting translation elongation factor 1 (TEF1). We also present the new primer pair Fa+7/Ra+6. MockFusariumcommunities reflecting phylogenetic diversity were used to evaluate the accuracy of the primers in reflecting the relative abundance of the species. TEF1 amplicons were subjected to 454 high-throughput sequencing to characterizeFusariumcommunities. Field samples from soil and wheat kernels were included to test the method on more-complex material. For kernel samples, a single PCR was sufficient, while for soil samples, nested PCR was necessary. The newly developed primer pairs Fa+7/Ra+6 and Fa/Ra accurately reflectedFusariumspecies composition in mock DNA communities. In field samples, 47Fusariumoperational taxonomic units were identified, with the highestFusariumdiversity in soil. TheFusariumcommunity in soil was dominated by members of theFusarium incarnatum-Fusarium equisetispecies complex, contradicting findings in previous studies. The method was successfully applied to analyzeFusariumcommunities in soil and plant material and can facilitate further studies ofFusariumecology.

scholarly journals Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems

2021 ◽  
Vol 9 (8) ◽  
pp. 1730
Author(s):  
Artemis Rumbou ◽  
Eeva J. Vainio ◽  
Carmen Büttner
Keyword(s):  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Plant Protection ◽  
Forest Health ◽  
Practical Applications ◽  
Fungal Plant Pathogens ◽  
Fungal Associates ◽  
Quantitative Impact ◽  
Symbiotic Microbiota

Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus–virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.

scholarly journals Urbanization pressures alter tree rhizosphere microbiomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Carl L. Rosier ◽  
Shawn W. Polson ◽  
Vincent D’Amico ◽  
Jinjun Kan ◽  
Tara L. E. Trammell
Keyword(s):  
Organic Matter ◽  
Relative Abundance ◽  
Tree Species ◽  
High Throughput Sequencing ◽  
Regional Climate ◽  
Keystone Species ◽  
Fagus Grandifolia ◽  
Yellow Poplar ◽  
Individual Tree ◽  
Structural Formation

AbstractThe soil microbial community (SMC) provides critical ecosystem services including organic matter decomposition, soil structural formation, and nutrient cycling. Studies suggest plants, specifically trees, act as soil keystone species controlling SMC structure via multiple mechanisms (e.g., litter chemistry, root exudates, and canopy alteration of precipitation). Tree influence on SMC is shaped by local/regional climate effects on forested environments and the connection of forests to surrounding landscapes (e.g., urbanization). Urban soils offer an ideal analog to assess the influence of environmental conditions versus plant species-specific controls on SMC. We used next generation high throughput sequencing to characterize the SMC of specific tree species (Fagus grandifolia [beech] vs Liriodendron tulipifera [yellow poplar]) across an urban–rural gradient. Results indicate SMC dissimilarity within rural forests suggests the SMC is unique to individual tree species. However, greater urbanization pressure increased SMC similarity between tree species. Relative abundance, species richness, and evenness suggest that increases in similarity within urban forests is not the result of biodiversity loss, but rather due to greater overlap of shared taxa. Evaluation of soil chemistry across the rural–urban gradient indicate pH, Ca+, and organic matter are largely responsible for driving relative abundance of specific SMC members.

scholarly journals The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marta Matuszewska ◽  
Tomasz Maciąg ◽  
Magdalena Rajewska ◽  
Aldona Wierzbicka ◽  
Sylwia Jafra
Keyword(s):  
Gene Expression ◽  
Antimicrobial Activity ◽  
Carbon Source ◽  
Reference Genes ◽  
Plant Pathogens ◽  
Plant Protection ◽  
Carbon Sources ◽  
Unknown Compound ◽  
Fungal Plant Pathogens ◽  
The Impact

AbstractPseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound (“cluster 17”) and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

A case of gender equality: absence of sex-related costs in a dioecious tropical forest tree species

Plant Ecology ◽  
2021 ◽  
Author(s):  
Valéria Forni Martins ◽  
Rafaela Letícia Brito Bispo ◽  
Priscilla de Paula Loiola
Keyword(s):  
Tropical Forest ◽  
Gender Equality ◽  
Tree Species ◽  
Forest Tree ◽  
Forest Tree Species
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