Best practices in metabarcoding of fungi: from experimental design to results

L Tedersoo, M Bahram, L Zinger, RH Nilsson… - Molecular …, 2022 - Wiley Online Library
The development of high‐throughput sequencing (HTS) technologies has greatly improved
our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems …

Ribosome biogenesis factors—from names to functions

K Dörner, C Ruggeri, I Zemp, U Kutay - The EMBO journal, 2023 - embopress.org
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge
cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified …

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

R Lücking, MC Aime, B Robbertse, AN Miller… - IMA fungus, 2020 - Springer
True fungi (Fungi) and fungus-like organisms (eg Mycetozoa, Oomycota) constitute the
second largest group of organisms based on global richness estimates, with around 3 …

Microbial diversity drives carbon use efficiency in a model soil

LA Domeignoz-Horta, G Pold, XJA Liu, SD Frey… - Nature …, 2020 - nature.com
Empirical evidence for the response of soil carbon cycling to the combined effects of
warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a …

[HTML][HTML] ITS alchemy: on the use of ITS as a DNA marker in fungal ecology

H Kauserud - Fungal Ecology, 2023 - Elsevier
High throughput sequencing of PCR amplicons derived from environmental DNA (aka DNA
metabarcoding) has become an integral part of fungal ecology, enabling in-depth …

The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here?

JG Harrison, EA Griffin - Environmental microbiology, 2020 - Wiley Online Library
The interiors of plants are colonized by diverse microorganisms that are referred to as
endophytes. Endophytes have received much attention over the past few decades, yet many …

Genetic determinants of endophytism in the Arabidopsis root mycobiome

F Mesny, S Miyauchi, T Thiergart, B Pickel… - Nature …, 2021 - nature.com
The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health
and disease states. Here, we sequence the genomes of 41 fungal isolates representative of …

Metschnikowia pulcherrima and Related Pulcherrimin-Producing Yeasts: Fuzzy Species Boundaries and Complex Antimicrobial Antagonism

M Sipiczki - Microorganisms, 2020 - mdpi.com
Yeasts affiliated with the Metschnikowia pulcherrima clade (subclade) of the large
ascomycetous genus Metschnikowia frequently turn out to produce the characteristic …

Does intraspecific variation in rDNA copy number affect analysis of microbial communities?

A Lavrinienko, T Jernfors, JJ Koskimäki, AM Pirttilä… - Trends in …, 2021 - cell.com
Amplicon sequencing of partial regions of the ribosomal RNA loci (rDNA) is widely used to
profile microbial communities. However, the rDNA is dynamic and can exhibit substantial …

Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves

J Regalado, DS Lundberg, O Deusch… - The ISME …, 2020 - academic.oup.com
Microorganisms from all domains of life establish associations with plants. Although some
harm the plant, others antagonize pathogens or prime the plant immune system, support the …