Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

KC Beng, RT Corlett - Biodiversity and conservation, 2020 - Springer
Conserving biodiversity in the face of ever-increasing human pressure is hampered by our
lack of basic information on species occurrence, distribution, abundance, habitat …

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 …

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

BE Deagle, AC Thomas, JC McInnes… - Molecular …, 2019 - Wiley Online Library
Advances in DNA sequencing technology have revolutionized the field of molecular analysis
of trophic interactions, and it is now possible to recover counts of food DNA sequences from …

Global negative effects of nitrogen deposition on soil microbes

T Zhang, HYH Chen, H Ruan - The ISME journal, 2018 - academic.oup.com
Soil microbes comprise a large portion of the genetic diversity on Earth and influence a large
number of important ecosystem processes. Increasing atmospheric nitrogen (N) deposition …

FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild

NH Nguyen, Z Song, ST Bates, S Branco, L Tedersoo… - Fungal ecology, 2016 - Elsevier
Fungi typically live in highly diverse communities composed of multiple ecological guilds.
Although high-throughput sequencing has greatly increased the ability to quantify the …

Accurate estimation of fungal diversity and abundance through improved lineage-specific primers optimized for Illumina amplicon sequencing

DL Taylor, WA Walters, NJ Lennon… - Applied and …, 2016 - journals.asm.org
While high-throughput sequencing methods are revolutionizing fungal ecology, recovering
accurate estimates of species richness and abundance has proven elusive. We sought to …

Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition

W Purahong, T Wubet, G Lentendu… - Molecular …, 2016 - Wiley Online Library
Microorganisms play a crucial role in the biological decomposition of plant litter in terrestrial
ecosystems. Due to the permanently changing litter quality during decomposition, studies of …

Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis

TM Porter, M Hajibabaei - Molecular ecology, 2018 - Wiley Online Library
The purpose of this review is to present the most common and emerging DNA‐based
methods used to generate data for biodiversity and biomonitoring studies. As environmental …

The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses

T Větrovský, P Baldrian - PloS one, 2013 - journals.plos.org
16S ribosomal RNA currently represents the most important target of study in bacterial
ecology. Its use for the description of bacterial diversity is, however, limited by the presence …

New primers to amplify the fungal ITS2 region–evaluation by 454-sequencing of artificial and natural communities

K Ihrmark, ITM Bödeker, K Cruz-Martinez… - FEMS microbiology …, 2012 - academic.oup.com
With recent methodological advances, molecular markers are increasingly used for semi-
quantitative analyses of fungal communities. The aim to preserve quantitative relationships …