Metabarcoding and Metagenomics

Biodiversity is declining in freshwater ecosystems, increasing the need for efficient monitoring tools. Environmental DNA (eDNA) is a powerful approach for detecting aquatic speci…

This study investigates the taxonomic composition, richness and diversity of microbial and metazoan communities in two adjacent ecosystems — a preserved Native Forest and a Highla…

Molecular techniques involving environmental DNA (eDNA) are increasingly used for aquatic species detection. Metabarcoding, a widely adopted technique, suffers from primer bias: u…

Microbial eukaryotes play a vital role in biogeochemical cycles and aquatic food webs. Over past decades, their taxonomic diversity has been investigated using short-read DNA meta…

Metabarcoding of vertebrate DNA derived from invertebrates (iDNA) is a promising method for monitoring of mammal assemblages. However, optimization of field and laboratory methods…

Metabarcoding offers a powerful approach for assessing benthic biodiversity in remote and understudied deep-sea environments. However, the methodological performance of different …

Environmental DNA (eDNA) is increasingly used in aquatic research and applied biodiversity monitoring, mainly through a metabarcoding approach. This allows detailed analyses of sp…

Integrating intercropping with green manure within crop rotation offers a sustainable pathway to enhance soil microbial diversity and overall agroecosystem health. This study eval…

Environmental DNA (eDNA) metabarcoding revolutionized the biodiversity monitoring in aquatic ecosystems, giving access to taxonomic lists in a non-disruptive way. Although the met…

DNA metabarcoding of zooplankton samples is well suited to surveys of marine pelagic ecosystems; however, consistent amplification across zooplankton groups cannot be assumed when…

Genetic sampling from European honeybee (Apis mellifera) hives is a promising repository of terrestrial environmental nucleic acids (eNA) from a range of taxonomic sources. eNA sa…

Environmental DNA (eDNA) metabarcoding of streams can deliver information on biological communities with minimally invasive efforts and at low costs. However, the captured eDNA ma…

Monitoring changes in freshwater fauna requires timely, efficient, and comprehensive data collection, needs that are increasingly met by molecular methods. This is especially impo…

Aedes aegypti poses a significant threat by transmitting diseases like dengue, chikungunya and Zika, leading to high morbidity and mortality worldwide. In recent years, the role o…

Environmental DNA (eDNA) techniques are increasingly employed in biodiversity monitoring of aquatic and terrestrial animals, plants, and fungi, holding great potential to revoluti…

DNA metabarcoding of benthic diatoms has been successfully applied for biomonitoring at the national scale and can now be considered technically ready for routine application. How…

Increasing livestock densities and more severe drought events challenge sustainable management in South Africa’s semi-arid savannas. Effective mitigation strategies require accura…

Unprecedented rates of biodiversity loss and ecosystem function necessitate the use of rapid, efficacious, and cost-effective biomonitoring tools. The combination of autonomous sa…

Sand nourishment is a common and often applied coastal protection measure along the beaches of the German Baltic Sea coast. At the tourist beach of Ahrenshoop, large-scale sand no…

Introduced trout can induce trophic cascades, however, a lack of pre-introduction data limits knowledge on their impact in many lakes. Traditional paleolimnological approaches hav…

Polar regions are among the most extreme habitats on Earth. However, diatom biodiversity in those regions is much more extensive and ecologically diverse than previously thought. …

Rhipicephalus sanguineus sensu lato (s.l.), commonly known as the domestic dog tick, is a globally distributed tick. This species plays a significant role in human and animal heal…

Due to anthropogenic influences, habitat degradation and a continuous loss of biodiversity in freshwater ecosystems are occurring on a large scale, while these ecosystems constitu…

Bird nests are fascinating microcosms harboring a wide range of arthropods parasitizing the nesting birds or feeding on prey remains, feces, and the nest material. Studies of thes…

Understanding how different taxa respond to abiotic characteristics of the environment is of key interest for understanding the assembly of communities. Yet, whether eDNA data wil…

A comprehensive understanding of trophic interactions in terrestrial ecosystems is crucial for ecological research and conservation. Recent advances in non-invasive methods, such …

Aquatic emergent insect communities form an important link between aquatic and terrestrial ecosystems, yet studying them is costly and time-consuming as they are usually diverse a…

Landscape changes, over time, lead to changes of floral resources available to pollinators, which in turn may result in the disappearance of ecologically specialized species. Here…

Brittle stars (class Ophiuroidea) are marine invertebrates comprising approximately 2,100 extant species, and are considered to constitute the most diverse taxon of the phylum Ech…

Implementation of DNA metabarcoding for diatoms for environmental monitoring is now moving from a research to an operational phase, requiring rigorous guidelines and standards. In…

Diatoms are valuable bioindicators and their traditional classification and identification are mainly based on the morphological characteristics of their frustules. However, in re…

Monitoring of artificial reefs (ARs) has been conducted through such methods as visual censuses, surveys using fishing gear, and echo sounder. These methods have disadvantages: vi…

During the recent decade, high-throughput sequencing (HTS) techniques, in particular, DNA metabarcoding, have facilitated increased detection of biodiversity, including harmful al…

Flowers are colonized and inhabited by diverse microbes. Flowers have various mechanisms to suppress microbial growth, such as flower volatiles, reactive oxygen and secondary comp…

In this data paper, we describe environmental DNA (eDNA) cytochrome c oxidase (COI) amplicon sequence data from New York City’s Bronx River Estuary. As urban systems continue to e…

Environmental DNA (eDNA) metabarcoding from water samples has, in recent years, shown great promise for biodiversity monitoring. However, universal primers targeting the cytochrom…

Increasing anthropogenic pressures on the coastal marine environments impact these ecosystems via a variety of mechanisms including nutrient loading, leading to eutrophication and…

To address the global biodiversity crisis, standardized data that are rapidly obtainable through minimally invasive means are needed for documenting change and informing conservat…

Molecular-based techniques offer considerable potential to provide new insights into the impact of anthropogenic stressors on lake ecosystems. Microbial communities are involved i…

Sagami Bay, Japan is influenced by both the warm Kuroshio Current and the cold Oyashio Current and rich nutrients are supplied from multiple river sources and the deep-sea, formin…

Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular…

DNA metabarcoding has great potential to improve marine biomonitoring programs by providing a rapid and accurate assessment of species composition in zoobenthic communities. Howev…

Longevity of species populations depends largely on interactions among animals and plants in an ecosystem. Predation and seed dispersal are among the most important interactions n…

Characterising and monitoring biological diversity to foster sustainable ecosystems is highly recommended as urban centres rapidly expand. However, much of New York City’s biodive…

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcod…

The use of toothbrushes and similar devices for sampling diatoms from hard surfaces is a well-established approach. Toothbrushes are routinely cleaned and reused when sampling for…

Robust data to refute or support claims of global insect decline are currently lacking, particularly for the soil fauna in the tropics. DNA metabarcoding represents a powerful app…

Storage of soil samples prior to metagenomic analysis presents a problem. If field sites are remote or if samples are collected by third parties, transport to analytical laborator…

Aquatic macroinvertebrates are often identified, based on morphology, but molecular approaches like DNA barcoding, metabarcoding and metagenomics are increasingly used for species…

For many organisms, there is agreement on the specific genomic region used for developing barcode markers. With nematodes, however, it has been found that the COI region designate…