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opencc-zeroFeb 2022View details →

Supplementary material 1 from: Gueidan C, Li L (2022) A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 86: 195-212. https://doi.org/10.3897/mycokeys.86.77431

Table S1. List of specimens used for this study, including their voucher information, plate location, indexing, amplicon concentration and sequencing results, both as an output from SMRT tools (CCSs) and as an output from DADA2 (sequence variants). Table S2. List of the 64 barcode sequences used to index the samples. Used barcode pairs are listed in Table S1

opencc-zeroFeb 2022View details →

Metabarcoding of the microbial community inhabiting the phosphogypsum stockpiles of the city of Huelva (SW, Spain)

In this work, metabarcoding of 16S and 18S rRNA gene coding sequences were employed to characterize the prokaryotic and eukaryotic communities in the phosphogypsum stacks located in the city of Huelva (SW Spain). In this environment around 100 Mt of phosphogypsum with extreme acidity and high concentrations of heavy metals and radionuclides have been accumulated for more than forty years on the marshlands of the Tinto River estuary. The microbial community inhabiting these adverse conditions remains unknown, although it can have an effect on the biogeochemical cycle of the phosphogypsum components and contain new species with biotechnological interest.

Supplementary material 6 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106

Table S2. Class level identification of OTUs showing the number of OTUs produced with ITS2 and LSU and the proportion of the total OTU set on the rarefied data

Supplementary material 5 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106

Table S1. Accession numbers corresponding with the reference sequences used to build the phylogenetic trees

Supplementary material 3 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106

Figure S3. Maximum-likelihood tree constructed in IQ-Tree2 based on three-gene (LSU D1-D2, SSU, ITS2) reference sequence alignments and OTUs for both markers (clustering thresholds: 99% LSU D1-D2 and 98% ITS2)

Supplementary material 2 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106

Figure S2. Species accumulation curves of the OTUs generated from the ITS (panel right) and LSU (panel left) metabarcodes

Raw sequence of: Field investigation- and dietary metabarcoding-based screening of arthropods that prey on primary tea pests

Predatory natural enemies play key functional roles in biological control. Abundant predatory arthropod species have been recorded in tea plantation ecosystems. However, few studies have comprehensively evaluated the control effect of predatory arthropods on tea pests in the field. We performed a one-year field investigation and collected predatory arthropods and pests in the tea canopy. Total 7,931 predatory arthropod individuals were collected, and Coleosoma blandum (Araneae, Theridiidae) was the most abundant species in the studied tea plantation. The population dynamics between C. blandum and four main tea pest species (Aleurocanthus spiniferus, Empoasca onukii, Ectropis grisescens and Scopula subpunctaria) were established using the individual number of predators and pests in each month. The results showed that the occurrence of C. blandum showed high synchronism with the occurrence of A. spiniferus, Em. onukii and Ec. grisescens. The prey spectrum of C. blandum was further analyzed using DNA metabarcoding. Among prey species, A. spiniferus, Em. onukii and Ec. grisescens were included, and the relative abundance and positive rates of target DNA fragments of A. spiniferus were obviously greater than those of other two pests.

Data from: Leveraging eDNA metabarcoding to characterize nearshore fish communities in Southeast Alaska: Do habitat and tide matter?

Nearshore marine habitats are critical for a variety of commercially important fish species, but assessing fish communities in these habitats is costly and time-intensive. Here, we leverage eDNA metabarcoding to characterize nearshore fish communities near Juneau, Alaska, USA, a high-latitude environment with large tidal swings, strong currents, and significant freshwater input. We investigated whether species richness and community composition differed across three habitat types (sand beaches, eelgrass beds, and rocky shorelines) and between high and low tides. Additionally, we tested whether replication of field samples and PCR reactions influenced either species richness or composition. We amplified a 12S mitochondrial locus in our samples and identified 167 fish amplicon sequence variants (ASVs), which were grouped into 24 unique taxa based on sequence similarity, with approximately half of these taxa resolved to single species. Species richness and composition inferred from eDNA differed substantially among habitats, with rock habitats containing fewer taxa and fewer overall detections than sand and eelgrass habitats. The effect of tide was not significant on its own, but a significant habitat-tide interaction was documented, with the most pronounced differences in taxa between tides found in sand habitats. Power analyses indicated that additional field sampling is useful to detect small changes in species richness such as those due to tide. PCR replicates typically identified few additional taxa. Our results provide important information that can be used to guide future studies, most notably, that the influence of tide on eDNA results appears to be minimal and potentially isolated to certain habitats. This suggests that replication across tides may not be vital for future eDNA studies, and that additional replication across space – particularly across heterogeneous environments – likely is a better allocation of sampling effort.

Supplementary material 1 from: Chua PYS, Carøe C, Crampton-Platt A, Reyes-Avila CS, Jones G, Streicker DG, Bohmann K (2022) A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus). Metabarcoding and Metagenomics 6: e78756. https://doi.org/10.3897/mbmg.6.78756

A two-step metagenomics approach for prey identification from the blood meals of common vampire bats (Desmodus rotundus)

opencc-by-4.0Apr 2022View details →

Supplement table of mesozooplankton taxa obtained using long-read and short-read metabarcoding

Supplement tables containing information about publications on mesozooplankton taxa in the Ross Sea using two metabarcoding analyses

DNA metabarcoding reveals broadly overlapping diets in three sympatric North American hummingbirds

Hummingbirds, a highly diverse avian family, are specialized vertebrate pollinators that feed upon carbohydrate-rich nectar to fuel their fast metabolism while consuming invertebrates to obtain protein. Previous work has found that morphologically diverse hummingbird communities exhibit higher diet specialization on floral resources than morphologically similar hummingbird communities. Due to the difficulties of studying avian diets, we have little understanding whether hummingbirds show similar patterns with their invertebrate prey. Here, we use DNA metabarcoding to complete an analysis of floral and invertebrate diets of three species of sympatric North American hummingbirds. We collected fecal samples from 89 Anna's (Calypte anna), 39 Black-chinned (Archilochus alexandri), and 29 Calliope (Selasphorus calliope) hummingbirds in urban and rural localities as well as across an elevational gradient from sea level to 2500 meters above sea level in California, USA. We found hummingbirds showed high dietary overlap in both invertebrate and plant resources, with few invertebrate and plant families common to most individuals and many families found in only a few individuals. Chironomidae was the most common invertebrate family across all species, and Rosaceae and Orobanchaceae were the most common plant families. Anna's Hummingbirds had significantly higher invertebrate diet diversity than Black-chinned Hummingbirds when found at the same sites, but we found no difference in plant diet diversity among any of the three species. Hummingbirds in urban sites had higher plant diet diversity than in rural sites, but we found no effect of elevation on dietary richness. Our study shows how DNA metabarcoding can be used to non-invasively investigate previously unknown life-histories of well-studied birds, lending insight to community structure, function, and evolution.

Data from: Community assembly and metaphylogeography of soil biodiversity: insights from haplotype-level community DNA metabarcoding within an oceanic island

Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here we take advantage of a relatively young and dynamic oceanic island to advance our understanding of eco-evolutionary processes driving community assembly within soil mesofauna. Using whole organism community DNA (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we have generated spatially explicit and reliable haplotype-level DNA sequence data for soil mesofauna assemblages sampled across the four main habitats within the island of Tenerife. Community ecological and metaphylogeographic analyses have been performed at multiple levels of genetic similarity, from haplotypes to species and supraspecific groupings. Broadly consistent patterns of local-scale species richness across different insular habitats have been found, whereas local insular richness is lower than in continental settings. Our results reveal an important role for niche conservatism as a driver of insular community assembly of soil mesofauna, with only limited evidence for habitat shifts promoting diversification. Furthermore, support is found for a fundamental role of habitat in the assembly of soil mesofauna, where habitat specialism is mainly due to colonisation and the establishment of preadapted species. Hierarchical patterns of distance decay at the community level and metaphylogeographical analyses support a pattern of geographic structuring over limited spatial scales, from the level of haplotypes through to species and lineages, as expected for taxa with strong dispersal limitations. Our results demonstrate the potential for wocDNA metabarcoding to advance our understanding of biodiversity.

opencc-by-4.0May 2022View details →

Supplement table of meso- and macrozooplankton taxa obtained using dual metabarcoding platforms in the Ross Sea

Supplement tables containing information about publications on meso- and marcozooplankton taxa in the Ross Sea using dual metabarcoding analyses (PacBio and MiSeq platforms)

opencc-zeroJun 2022View details →

Supplementary material 3 from: Jeunen G-J, Lipinskaya T, Gajduchenko H, Golovenchik V, Moroz M, Rizevsky V, Semenchenko V, Gemmell NJ (2022) Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe. Metabarcoding and Metagenomics 6: e68575. https://doi.org/10.3897/mbmg.6.e68575

Reference databases generated by ecoPCR and used by ecotag for taxonomy assignment of OTUs for fish and crustacean eDNA results

opencc-zeroDec 2011View details →

Data from: Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

1) Traditional biodiversity assessment is costly in time, money, and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution. 2) We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass-PCR amplification of the COI barcode gene, pyrosequencing, and bioinformatic analysis, which together we call 'metabarcoding.' 3) We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding. 4) Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.

opencc-by-4.0Jul 2022View details →

16S metabarcoding tutorial

Tutorial for the analysis of 16S rRNA metabarcoding sequences using the MiSeq SOP pipeline. https://github.com/AndresICM/16S-rRNA-Metabarcoding-analysis

opencc-zeroJul 2022View details →

DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity

Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (I) spatial and temporal connectivity of the communities, (II) environmental factors influencing local communities, and (III) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.

opencc-zeroJul 2022View details →

Supplementary material 3 from: Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B (2022) The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. Metabarcoding and Metagenomics 6: e85213. https://doi.org/10.3897/mbmg.6.85213

Supplementary material 3 from: Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B (2022) The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. Metabarcoding and Metagenomics 6: e85213. https://doi.org/10.3897/mbmg.6.85213

opencc-zeroAug 2022View details →

Relationship between eDNA concentration from metabarcoding method and stream fish density under field conditions

Estimating abundance or biomass using eDNA metabarcoding is a powerful emerging tool that may provide an alternative to conventional laborious methods for biological monitoring. However, inferring aquatic macroorganism abundance or biomass using eDNA concentrations remains challenging, especially in lotic environments, because of several potential confounding factors. In this study, we tested whether quantitative eDNA metabarcoding that uses internal standard DNA can be used to estimate the abundance of four fish species. We collected eDNA samples and concurrently estimated fish densities using the conventional removal method in small tributaries in four seasons during a year. The effects of potential confounding factors, including the body mass of the individuals, water temperature, and discharge volume, were assessed using an allometric scaling model. We found an increasing trend of eDNA concentration against the increase in abundance across all species. In the most abundant species, a significant increase in the precision of predicted abundance was achieved by considering confounding factors, such as season and discharge. Although this study successfully determined the relationships between eDNA concentration and fish abundance under lotic field conditions, it also identified several limitations of quantitative eDNA metabarcoding. The relationship between eDNA concentration and fish abundance in rare species showed significant variances in the regression. More sequencing depth may be necessary to detect rare species sufficiently. The eDNA concentration estimation error effect was significant, particularly among the samples that showed the same abundance figures by direct capture estimation. The utilization of quantitative eDNA metabarcoding may be suitable for organisms that are expected to have a substantial variation in their population density. More comparative studies with various conventional methods would be informative, especially in lotic field environments, to overcome these limitations and achieve wider applications of eDNA metabarcoding in future research and monitoring.