Advanced research tools for fungal diversity and its impact on forest ecosystem

Adnan, Muhammad; Islam, Waqar; Liu, Gang; Chen, Han Y. H.

doi:10.1007/s11356-022-20317-8

Cited by 17 publications

(15 citation statements)

References 205 publications

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“…Applicable in non-model species, cost-effective Potentially missing low-abundance transcripts Weber (2015); Harper et al (2016); Holliday et al (2019); Wu et al (2019); Zinkgraf et al (2020) functional and ecological attributes (e.g., Adnan et al 2022;Genre et al 2020;Holliday et al 2019;Isabel et al 2020;Lind et al 2018;Nilsson et al 2019;Plomion et al 2016).…”

Section: Analyses Of Full Genomesmentioning

confidence: 99%

“…by insect vectors or from the aeromycota to phyllospheres shape host-, organ-and vertical-stratification-specific but yet little-analyzed communities on the aerial surfaces of tree organs Saprotrophs of recalcitrant dead organic material (mostly kinds of above and belowground plant litter and deadwood, each with its own shaped sets of fungal communities; Fig. 1) will ensure humus generation and, of imminent importance for the trees, the recycling of bound organic carbon and further elements needed for new plant growth (Adnan et al 2022;Bödeker et al 2016;Floudas et al 2012Floudas et al , 2020Kües et al in prep.). Dead plant litter is complex and diverse in composition, context-dependent by habitat and plant source.…”

Section: Fungal Guilds Living In Interactions With Treesmentioning

confidence: 99%

“…Accordingly, the phytobiome encompasses the plant, its environment, and all organisms living in, on, and around the plant. Environments are not static and trees are thus confronted manifold with changing biotic and abiotic influences (e.g., Adnan et al 2022 ; Fortier et al 2019 ; Frei et al 2018 ; Teshome et al 2020 ; Fig. 1 ).…”

Section: Introductionmentioning

confidence: 99%

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Applying molecular and genetic methods to trees and their fungal communities

Müller

Kües

Budde

et al. 2023

Appl Microbiol Biotechnol

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Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. Key points • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.

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Section: Analyses Of Full Genomesmentioning

confidence: 99%

Section: Fungal Guilds Living In Interactions With Treesmentioning

confidence: 99%

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Applying molecular and genetic methods to trees and their fungal communities

Müller

Kües

Budde

et al. 2023

Appl Microbiol Biotechnol

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“…Biological particles, along with inorganic gaseous and particulate pollutants, constitute an ever-present component of the atmosphere and surfaces. Among these bioparticles are fungal spores and hyphae [ 1 , 2 ] that colonize almost all terrestrial [ 3 ] and aquatic ecosystems [ 4 , 5 ], and even the inside and outside of the human body [ 6 , 7 , 8 ]. This diverse kingdom is composed of approximately 150,000 known species, and it is estimated that nearly a thousand times more species are yet to be described [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Clinical Manifestations of Human Exposure to Fungi

Oliveira

Lisboa

et al. 2023

JoF

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Biological particles, along with inorganic gaseous and particulate pollutants, constitute an ever-present component of the atmosphere and surfaces. Among these particles are fungal species colonizing almost all ecosystems, including the human body. Although inoffensive to most people, fungi can be responsible for several health problems, such as allergic fungal diseases and fungal infections. Worldwide fungal disease incidence is increasing, with new emerging fungal diseases appearing yearly. Reasons for this increase are the expansion of life expectancy, the number of immunocompromised patients (immunosuppressive treatments for transplantation, autoimmune diseases, and immunodeficiency diseases), the number of uncontrolled underlying conditions (e.g., diabetes mellitus), and the misusage of medication (e.g., corticosteroids and broad-spectrum antibiotics). Managing fungal diseases is challenging; only four classes of antifungal drugs are available, resistance to these drugs is increasing, and no vaccines have been approved. The present work reviews the implications of fungal particles in human health from allergic diseases (i.e., allergic bronchopulmonary aspergillosis, severe asthma with fungal sensitization, thunderstorm asthma, allergic fungal rhinosinusitis, and occupational lung diseases) to infections (i.e., superficial, subcutaneous, and systemic infections). Topics such as the etiological agent, risk factors, clinical manifestations, diagnosis, and treatment will be revised to improve the knowledge of this growing health concern.

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“…When considering the biodiversity on Earth, Fungi are the third most diverse group of eukaryotic organisms, with approximately 140,000 known species, although the estimates can be as low as 700,000 and as high as 12 million [ 1 , 2 , 3 , 4 ]. Fungi can be found in terrestrial, e.g., [ 5 ], freshwater, e.g., [ 6 ] and marine ecosystems, e.g., [ 7 ]. In these ecosystems these organisms are important pathogens for humans, animal and plants, and also important carbon and nutrient recycling agents [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years

Oliveira

Azevedo

2022

JoF

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Fungi are amongst the most abundant and diverse organisms. Despite being widely known for their adverse role in food spoilage or as pathogens for humans, animals, or plants, they also present several beneficial effects. Fungi contribute to human well-being due to their role as decomposers, degrading decay matter into smaller molecules which can be easily used by other ecosystem members. These organisms can produce medicinal compounds or modulate protective immune responses in human intestine. Fungi intervene in diverse food processes or act as a food supply. Due to fungal diversity, the unequivocal identification of these organisms is crucial to increasing their practical applications and decreasing their adverse effects. The process of identification could be achieved through the integral sequencing of fungi genomes. However, this procedure would be time-consuming and rather cost-inefficient. Therefore, several molecular markers have been developed to overcome these limitations. The chronology of DNA-based molecular markers development can be divided into three main steps: (1) prior to the development of the PCR technique (RFLP); (2) after the development of the PCR technique (RAPD, AFLP, ISSR, VNTR, SNP, InDels, and DNA barcoding); (3) after the development of the massive parallel sequencing technique (Metabarcoding and WGS). Therefore, the present review covers an overview of the most recently developed molecular markers used for fungal detection and identification.

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Advanced research tools for fungal diversity and its impact on forest ecosystem

Cited by 17 publications

References 205 publications

Applying molecular and genetic methods to trees and their fungal communities

Applying molecular and genetic methods to trees and their fungal communities

Clinical Manifestations of Human Exposure to Fungi

Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years

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