Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities

GP Huston, MLD Lopez, Y Cheng, L King… - Environmental …, 2023 - Wiley Online Library
Environmental DNA studies have proliferated over the last decade, with promising data
describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The …

Current Utilization and Further Application of Zooplankton Indices for Ecosystem Health Assessment of Lake Ecosystems

Y Choi, HJ Oh, DH Lee, MH Jang, KL Lee, KH Chang… - Sustainability, 2023 - mdpi.com
For the sustainable use of lake ecosystem services—water resources, aquatic habitats for
biodiversity conservation, and aesthetic values as waterfront space—ecosystem health …

MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences

M Leray, N Knowlton, RJ Machida - Environmental DNA, 2022 - Wiley Online Library
Abstract Analysis of environmental DNA is increasingly used to characterize ecological
communities, but the effectiveness of this approach depends on the accuracy of taxonomic …

Higher N2O production in sequencing batch reactors compared to continuous stirred tank reactors: effect of feast-famine cycles

X Yan, X Shen, J Wang, J Zhuang, Y Wang… - … Science & Engineering, 2023 - Springer
Nitrous oxide (N2O) is a potent greenhouse gas that can be emitted during the biological
treatment of wastewater. In this study, a comparison of the long-term performance …

Allometric scaling of interspecific RNA transcript abundance to extend the use of metatranscriptomics in characterizing complex communities

MLD Lopez, Y Lin, SQ Schneider… - Molecular Ecology …, 2023 - Wiley Online Library
Metatranscriptomics allows profiling of community mRNA and rRNA transcript abundance
under certain environmental conditions. However, variations in the proportion of RNA …

Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller‐size coral reef …

FMG Mattos, N Dreyer, CL Fong… - Molecular Ecology …, 2024 - Wiley Online Library
PCR‐based high‐throughput sequencing has permitted comprehensive resolution analyses
of zooplankton diversity dynamics. However, significant methodological issues still surround …

Development of transcriptomics‐based growth rate indices in two model eukaryotes and relevance to metatranscriptomics datasets

WL Kong, RJ Machida - Molecular Ecology Resources, 2022 - Wiley Online Library
Growth rate estimation is important to understand the flow of energy and nutrient elements in
an ecosystem, but it has remained challenging, especially on microscopic organisms. In this …

Comparative analysis of zooplankton diversity in freshwaters: What can we gain from metagenomic analysis?

MÈ Monchamp, DA Walsh, RE Garner… - Environmental …, 2022 - Wiley Online Library
Molecular genetic approaches applied to environmental DNA have great potential for
biodiversity research and ecosystem monitoring. A metagenome is produced via shotgun …

Seasonal metabolic dynamics of microeukaryotic plankton: a year-long metatranscriptomic study in a temperate sea

M Perneel, R Lagaisse, J Mortelmans, S Maere… - MBio, 2024 - journals.asm.org
Seasonal fluctuations profoundly affect marine microeukaryotic plankton composition and
metabolism, but accurately tracking these changes has been a long-standing challenge. In …

Long-term archival of environmental samples empowers biodiversity monitoring and ecological research

VMA Zizka, J Koschorreck, CC Khan… - Environmental Sciences …, 2022 - Springer
Human-induced biodiversity loss and changes in community composition are major
challenges of the present time, urgently calling for comprehensive biomonitoring …