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 …

Mycobiome diversity: high-throughput sequencing and identification of fungi

RH Nilsson, S Anslan, M Bahram… - Nature Reviews …, 2019 - nature.com
Fungi are major ecological players in both terrestrial and aquatic environments by cycling
organic matter and channelling nutrients across trophic levels. High-throughput sequencing …

[HTML][HTML] Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

J Pawlowski, K Bruce, K Panksep, FI Aguirre… - Science of the Total …, 2022 - Elsevier
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for
identification of whole communities within a targeted group) is revolutionizing the field of …

Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes

JE Littlefair, LE Hrenchuk, PJ Blanchfield… - Molecular …, 2021 - Wiley Online Library
Significant advances have been made towards surveying animal and plant communities
using DNA isolated from environmental samples. Despite rapid progress, we lack a …

Invasive earthworms alter forest soil microbiomes and nitrogen cycling

J Jang, X Xiong, C Liu, K Yoo, S Ishii - Soil Biology and Biochemistry, 2022 - Elsevier
Northern hardwood forests in formerly glaciated areas had been free of earthworms until
exotic European earthworms were introduced by human activities. The invasion of exotic …

The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks

H Morita, S Akao - PLoS One, 2021 - journals.plos.org
To determine the optimal soil sample size for microbial community structure analysis, DNA
extraction, microbial composition analysis, and diversity assessments were performed using …

Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA

F Maixner, C Mitterer, HY Jäger… - Methods in Ecology …, 2022 - Wiley Online Library
Nucleic acid extraction from complex environmental and ancient tissue material is prone to
co‐extract inhibitory substances that make further molecular analysis difficult or impossible …

Standardization of plant microbiome studies: Which proportion of the microbiota is really harvested?

AR Sare, G Stouvenakers, M Eck, A Lampens… - Microorganisms, 2020 - mdpi.com
Studies in plant-microbiome currently use diverse protocols, making their comparison
difficult and biased. Research in human microbiome have faced similar challenges, but the …

Fungal degradation of complex organic carbon supports denitrification in saturated woodchip bioreactors

H Wang, GW Feyereisen, J Zhang, S Ishii - Bioresource Technology, 2025 - Elsevier
Woodchip bioreactor (WBR) is a promising technology for the removal of nitrate from
agricultural drainage, although the performance of WBRs is dependent on the …

Pitfalls and pointers: an accessible guide to marker gene amplicon sequencing in ecological applications

A Porath‐Krause, AT Strauss… - Methods in Ecology …, 2022 - Wiley Online Library
Abstract Next‐Generation Sequencing (NGS) is a powerful tool that has been rapidly
adopted by many ecologists studying microbial communities. Despite the exciting …