Subjects -> ENVIRONMENTAL STUDIES (Total: 913 journals)
    - ENVIRONMENTAL STUDIES (810 journals)
    - POLLUTION (31 journals)
    - TOXICOLOGY AND ENVIRONMENTAL SAFETY (54 journals)
    - WASTE MANAGEMENT (18 journals)

ENVIRONMENTAL STUDIES (810 journals)            First | 1 2 3 4 5     

Showing 401 - 378 of 378 Journals sorted alphabetically
International Journal of Environment and Sustainable Development     Hybrid Journal   (Followers: 17)
International Journal of Environment and Waste Management     Hybrid Journal   (Followers: 2)
International Journal of Environment, Workplace and Employment     Hybrid Journal   (Followers: 7)
International Journal of Environmental Engineering     Hybrid Journal   (Followers: 6)
International Journal of Environmental Health Engineering     Open Access   (Followers: 1)
International Journal of Environmental Health Research     Hybrid Journal   (Followers: 3)
International Journal of Environmental Policy and Decision Making     Hybrid Journal   (Followers: 3)
International Journal of Environmental Research     Hybrid Journal  
International Journal of Environmental Research and Public Health     Open Access   (Followers: 22)
International Journal of Environmental Science and Technology     Hybrid Journal   (Followers: 5)
International Journal of Environmental Studies     Hybrid Journal   (Followers: 5)
International Journal of Exergy     Hybrid Journal   (Followers: 2)
International Journal of Global Environmental Issues     Hybrid Journal   (Followers: 4)
International Journal of Global Sustainability     Open Access   (Followers: 2)
International Journal of Global Warming     Hybrid Journal  
International Journal of Greenhouse Gas Control     Partially Free   (Followers: 5)
International Journal of Hygiene and Environmental Health     Hybrid Journal   (Followers: 7)
International Journal of Logistics Research and Applications : A Leading Journal of Supply Chain Management     Hybrid Journal   (Followers: 16)
International Journal of Mining and Geo-Engineering     Open Access  
International Journal of Phytoremediation     Hybrid Journal   (Followers: 1)
International Journal of Process Systems Engineering     Hybrid Journal   (Followers: 1)
International Journal of Recycling of Organic Waste in Agriculture     Open Access   (Followers: 1)
International Journal of Reliability and Safety     Hybrid Journal   (Followers: 11)
International Journal of Renewable Energy Development     Open Access   (Followers: 6)
International Journal of Social Sciences and Management     Open Access   (Followers: 2)
International Journal of Soil, Sediment and Water     Open Access   (Followers: 4)
International Journal of Stress Management     Full-text available via subscription   (Followers: 6)
International Journal of Sustainable Construction Engineering and Technology     Open Access   (Followers: 7)
International Journal of Sustainable Engineering     Hybrid Journal   (Followers: 4)
International Journal of Sustainable Materials and Structural Systems     Hybrid Journal   (Followers: 1)
International Journal of Sustainable Society     Hybrid Journal   (Followers: 2)
International Journal of the Commons     Open Access   (Followers: 2)
International Journal of Toxicology     Hybrid Journal   (Followers: 17)
International Journal of Water Resources and Environmental Engineering     Open Access   (Followers: 11)
International Review of Environmental and Resource Economics     Full-text available via subscription   (Followers: 4)
Iranian Journal of Health and Environment     Open Access  
ISLE: Interdisciplinary Studies in Literature and Environment     Hybrid Journal   (Followers: 3)
Isotopes in Environmental and Health Studies     Hybrid Journal  
JACEE (Journal of Advanced Civil and Environmental Engineering)     Open Access  
Jahangirnagar University Environmental Bulletin     Open Access  
Journal for the History of Environment and Society     Open Access   (Followers: 3)
Journal of Bioremediation & Biodegradation     Open Access   (Followers: 1)
Journal of Earth Science & Climatic Change     Open Access   (Followers: 14)
Journal of Petroleum & Environmental Biotechnology     Open Access   (Followers: 1)
Journal of Advances in Environmental Health Research     Open Access   (Followers: 2)
Journal Of Advances In Natural Sciences     Open Access   (Followers: 1)
Journal of Aging and Environment     Hybrid Journal   (Followers: 4)
Journal of Agricultural and Environmental Ethics     Hybrid Journal   (Followers: 8)
Journal of Agricultural Chemistry and Environment     Open Access   (Followers: 3)
Journal of Agriculture and Ecology Research International     Open Access  
Journal of Air Pollution and Health (رتبه علمی- پژوهشی)     Open Access  
Journal of Anatolian Environmental and Animal Sciences     Open Access  
Journal of Applied Ecology     Hybrid Journal   (Followers: 205)
Journal of Applied Meteorology and Climatology     Hybrid Journal   (Followers: 42)
Journal of Applied Sciences and Environmental Management     Open Access   (Followers: 1)
Journal of Applied Toxicology     Hybrid Journal   (Followers: 19)
Journal of Applied Volcanology     Open Access   (Followers: 7)
Journal of Applied Water Engineering and Research     Hybrid Journal  
Journal of Arid Environments     Hybrid Journal   (Followers: 12)
Journal of Biochemical and Molecular Toxicology     Hybrid Journal   (Followers: 4)
Journal of Biosystems Engineering     Full-text available via subscription  
Journal of Chemical Ecology     Hybrid Journal   (Followers: 4)
Journal of Civil Engineering and Environmental Sciences     Open Access  
Journal of Climate     Hybrid Journal   (Followers: 56)
Journal of Climate Change and Health     Open Access   (Followers: 4)
Journal of Coastal Research     Hybrid Journal   (Followers: 31)
Journal of Contaminant Hydrology     Hybrid Journal   (Followers: 19)
Journal of Earth, Environment and Health Sciences     Open Access   (Followers: 2)
Journal of East African Natural History     Full-text available via subscription   (Followers: 7)
Journal of Ecology     Hybrid Journal   (Followers: 134)
Journal of Ecology and Environment     Open Access   (Followers: 3)
Journal of Economic Development, Environment and People     Open Access   (Followers: 11)
Journal of Energy & Natural Resources Law     Hybrid Journal   (Followers: 5)
Journal of Energy and Environment Technology of Graduate School Siam Technology College     Open Access  
Journal of Environment and Earth Science     Open Access   (Followers: 11)
Journal of Environment and Ecology     Open Access   (Followers: 10)
Journal of Environment Pollution and Human Health     Open Access   (Followers: 3)
Journal of Environmental Analysis and Progress     Open Access  
Journal of Environmental and Agricultural Studies     Open Access   (Followers: 1)
Journal of Environmental and Public Health     Open Access   (Followers: 16)
Journal of Environmental Assessment Policy and Management     Hybrid Journal   (Followers: 5)
Journal of Environmental Chemical Engineering     Hybrid Journal   (Followers: 5)
Journal of Environmental Economics and Policy     Partially Free   (Followers: 4)
Journal of Environmental Education     Hybrid Journal   (Followers: 7)
Journal of Environmental Engineering and Landscape Management     Open Access   (Followers: 8)
Journal of Environmental Engineering and Science     Hybrid Journal   (Followers: 2)
Journal of Environmental Extension     Full-text available via subscription  
Journal of Environmental Geography     Open Access   (Followers: 6)
Journal of Environmental Law     Hybrid Journal   (Followers: 22)
Journal of Environmental Management     Hybrid Journal   (Followers: 44)
Journal of Environmental Management     Open Access   (Followers: 1)
Journal of Environmental Management and Tourism     Open Access   (Followers: 13)
Journal of Environmental Media     Hybrid Journal  
Journal of Environmental Planning and Management     Hybrid Journal   (Followers: 26)
Journal of Environmental Policy & Planning     Hybrid Journal   (Followers: 14)
Journal of Environmental Professionals Sri Lanka     Open Access  
Journal of Environmental Protection     Open Access   (Followers: 1)
Journal of Environmental Science and Health, Part A: Toxic/Hazardous Substances and Environmental Engineering     Hybrid Journal   (Followers: 5)
Journal of Environmental Science and Health, Part B: Pesticides, Food Contaminants, and Agricultural Wastes     Hybrid Journal   (Followers: 5)
Journal of Environmental Science and Technology     Open Access   (Followers: 7)
Journal of Environmental Sciences     Full-text available via subscription   (Followers: 8)
Journal of Environmental Statistics     Open Access   (Followers: 4)
Journal of Environmental Studies and Sciences     Partially Free   (Followers: 2)
Journal of Environmental Sustainability     Open Access   (Followers: 7)
Journal of Environments     Open Access  
Journal of Exposure Science and Environmental Epidemiology     Hybrid Journal   (Followers: 6)
Journal of Fisheries and Environment     Open Access  
Journal of Forest and Natural Resource Management     Open Access  
Journal of Freshwater Ecology     Hybrid Journal   (Followers: 14)
Journal of Geography, Environment and Earth Science International     Open Access  
Journal of Geoscience and Environment Protection     Open Access  
Journal of Great Lakes Research     Hybrid Journal   (Followers: 5)
Journal of Green Building     Full-text available via subscription   (Followers: 10)
Journal of Hazardous Materials     Hybrid Journal   (Followers: 12)
Journal of Hazardous Materials Advances     Open Access  
Journal of Health Management     Hybrid Journal   (Followers: 10)
Journal of Health Organisation and Management     Hybrid Journal   (Followers: 29)
Journal of Housing and the Built Environment     Hybrid Journal   (Followers: 8)
Journal of Human Behavior in the Social Environment     Hybrid Journal   (Followers: 6)
Journal of Hydrology X     Open Access   (Followers: 5)
Journal of Industrial Ecology     Hybrid Journal   (Followers: 17)
Journal of Integrative Environmental Sciences     Hybrid Journal   (Followers: 4)
Journal of International Maritime Safety, Environmental Affairs, and Shipping     Open Access   (Followers: 1)
Journal of Iron and Steel Research International     Hybrid Journal   (Followers: 7)
Journal of Korean Society of Environmental Engineers     Open Access  
Journal of Land Use Science     Hybrid Journal   (Followers: 3)
Journal of Management and Sustainability     Open Access   (Followers: 7)
Journal of Mega Infrastructure & Sustainable Development     Hybrid Journal  
Journal of Natural Resources and Development     Open Access   (Followers: 2)
Journal of Natural Sciences Research     Open Access   (Followers: 1)
Journal of Occupational and Environmental Hygiene     Hybrid Journal   (Followers: 6)
Journal of Operational Oceanography     Hybrid Journal   (Followers: 5)
Journal of Organizational Behavior     Hybrid Journal   (Followers: 61)
Journal of Outdoor and Environmental Education     Hybrid Journal   (Followers: 2)
Journal of Pharmacological and Toxicological Methods     Hybrid Journal   (Followers: 7)
Journal of Plant Science and Phytopathology     Open Access  
Journal of Policy Analysis and Management     Hybrid Journal   (Followers: 28)
Journal of Population and Sustainability     Open Access  
Journal of Reliable Intelligent Environments     Hybrid Journal  
Journal of Renewable and Sustainable Energy     Hybrid Journal   (Followers: 11)
Journal of Research in Forestry, Wildlife and Environment     Open Access   (Followers: 5)
Journal of Rural and Community Development     Open Access   (Followers: 1)
Journal of Safety Engineering     Open Access   (Followers: 37)
Journal of Safety Research     Hybrid Journal   (Followers: 89)
Journal of School Violence     Hybrid Journal   (Followers: 6)
Journal of Sustainability and Environmental Management     Open Access   (Followers: 1)
Journal of Sustainable Development     Open Access   (Followers: 24)
Journal of Sustainable Development Studies     Open Access   (Followers: 15)
Journal of Sustainable Society     Open Access   (Followers: 2)
Journal of the American Planning Association     Hybrid Journal   (Followers: 18)
Journal of the Atmospheric Sciences     Hybrid Journal   (Followers: 83)
Journal of Tropical Ecology     Hybrid Journal   (Followers: 15)
Journal of Urban and Environmental Engineering     Open Access   (Followers: 5)
Journal of Urban Ecology     Open Access   (Followers: 5)
Journal of Vietnamese Environment     Open Access   (Followers: 1)
Journal of Water and Environmental Nanotechnology     Open Access   (Followers: 1)
Journal of Water Security     Open Access   (Followers: 6)
Julius-Kühn-Archiv     Open Access  
Jurnal Kesehatan Lingkungan     Open Access  
Jurnal Manusia dan Lingkungan     Open Access  
Jurnal Pengendalian Pencemaran Lingkungan     Open Access  
Jurnal Presipitasi     Open Access   (Followers: 1)
Jurnal Rekayasa Kimia & Lingkungan     Open Access  
Jurnal Sains & Teknologi Lingkungan     Open Access  
Jurnal Wilayah dan Lingkungan     Open Access  
Knowledge Management Research & Practice     Hybrid Journal   (Followers: 16)
Koedoe : African Protected Area Conservation and Science     Open Access   (Followers: 2)
Lake and Reservoir Management     Hybrid Journal   (Followers: 7)
Landscape Ecology     Hybrid Journal   (Followers: 61)
Landscapes     Hybrid Journal   (Followers: 18)
Latin American Journal of Management for Sustainable Development     Hybrid Journal  
Letras Verdes. Revista Latinoamericana de Estudios Socioambientales     Open Access  
Limnological Review     Open Access   (Followers: 3)
Living Reviews in Landscape Research     Open Access  
Local Environment: The International Journal of Justice and Sustainability     Hybrid Journal   (Followers: 8)
Low Carbon Economy     Open Access   (Followers: 4)
Luna Azul     Open Access  
M+A. Revista Electrónica de Medioambiente     Open Access  
Macquarie Journal of International and Comparative Environmental Law     Full-text available via subscription   (Followers: 7)
Madagascar Conservation & Development     Open Access   (Followers: 2)
Management International Review     Hybrid Journal   (Followers: 7)
Management of Environmental Quality: An International Journal     Hybrid Journal   (Followers: 2)
Management of Sustainable Development     Open Access   (Followers: 4)
Marine Ecology     Hybrid Journal   (Followers: 27)
Marine Ecology Progress Series MEPS     Hybrid Journal   (Followers: 34)
Marine Environmental Research     Hybrid Journal   (Followers: 31)
Marine Pollution Bulletin     Hybrid Journal   (Followers: 35)
Materials for Renewable and Sustainable Energy     Open Access   (Followers: 6)
Medio Ambiente y Urbanizacion     Full-text available via subscription  
Mediterranean Geoscience Reviews     Hybrid Journal  
Membranes     Open Access   (Followers: 3)
Metabarcoding and Metagenomics     Open Access  
Michigan Journal of Sustainability     Open Access   (Followers: 1)
Microbial Risk Analysis     Full-text available via subscription  
Microplastics and Nanoplastics     Open Access   (Followers: 1)
Mine Water and the Environment     Hybrid Journal   (Followers: 4)
Mitigation and Adaptation Strategies for Global Change     Open Access   (Followers: 8)
Modeling Earth Systems and Environment     Hybrid Journal   (Followers: 1)
Monteverdia     Open Access   (Followers: 1)
Multequina     Open Access  

  First | 1 2 3 4 5     

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Metabarcoding and Metagenomics
Number of Followers: 0  

  This is an Open Access Journal Open Access journal
ISSN (Online) 2534-9708
Published by Pensoft Homepage  [58 journals]
  • A triad of kicknet sampling, eDNA metabarcoding, and predictive
           modeling to assess richness of mayflies, stoneflies and caddisflies in
           rivers

    • Abstract: Metabarcoding and Metagenomics 6: e79351
      DOI : 10.3897/mbmg.6.79351
      Authors : François Keck, Samuel Hürlemann, Nadine Locher, Christian Stamm, Kristy Deiner, Florian Altermatt : Monitoring biodiversity is essential to understand the impacts of human activities and for effective management of ecosystems. Thereby, biodiversity can be assessed through direct collection of targeted organisms, through indirect evidence of their presence (e.g. signs, environmental DNA, camera trap, etc.), or through extrapolations from species distribution and species richness models. Differences in approaches used in biodiversity assessment, however, may come with individual challenges and hinder cross-study comparability. In the context of rapidly developing techniques, we compared three different approaches in order to better understand assessments of aquatic macroinvertebrate diversity. Specifically, we compared the community composition and species richness of three orders of aquatic macroinvertebrates (mayflies, stoneflies, and caddisflies, hereafter EPT) obtained via eDNA metabarcoding and via traditional in situ kicknet sampling to catchment-level based predictions of a species richness model. We used kicknet data from 24 sites in Switzerland and compared taxonomic lists to those obtained using eDNA amplified with two different primer sets. Richness detected by these methods was compared to the independent predictions made by a statistical species richness model, that is, a generalized linear model using landscape-level features to estimate EPT diversity. Despite the ability of eDNA to consistently detect some EPT species found by traditional sampling, we found important discrepancies in community composition between the kicknet and eDNA approaches, particularly at a local scale. We found the EPT-specific primer set fwhF2/EPTDr2n, detected a greater number of targeted EPT species compared to the more general primer set mlCOIintF/HCO2198. Moreover, we found that the species richness measured by eDNA from either primer set was poorly correlated to the richness measured by kicknet sampling (Pearson correlation = 0.27) and that the richness estimated by eDNA and kicknet were poorly correlated with the prediction of the species richness model (Pearson correlation = 0.30 and 0.44, respectively). The weak relationships between the traditional kicknet sampling and eDNA with this model indicates inherent limitations in upscaling species richness estimates, and possibly a limited ability of the model to meet real world expectations. It is also possible that the number of replicates was not sufficient to detect ambiguous correlations. Future challenges include improving the accuracy and sensitivity of each approach individually, yet also acknowledging their respective limitations, in order to best meet stakeholder demands and address the biodiversity crisis we are facing. HTML XML PDF
      PubDate: Tue, 10 May 2022 17:31:17 +030
       
  • Comparative metagenomics of phytoplankton blooms after nutrient
           enrichment of oligotrophic marine waters

    • Abstract: Metabarcoding and Metagenomics 6: e79208
      DOI : 10.3897/mbmg.6.79208
      Authors : John K. Pearman, Laura Casas, Craig Michell, Naroa Aldanondo, Nazia Mojib, Karie Holtermann, Ioannis Georgakakis, Joao Curdia, Susana Carvalho, Amr Gusti, Xabier Irigoien : Increasing anthropogenic pressures on the coastal marine environments impact these ecosystems via a variety of mechanisms including nutrient loading, leading to eutrophication and increases in algal blooms. Here, we use a metagenomics approach to assess the taxonomic and functional changes of the microbial community throughout a nutrient enriched mesocosm phytoplankton bloom. We tested four different nutrient treatments consisting of either nitrate and phosphate or nitrate, phosphate and silicate, administered on the first day or continuously for the first two weeks of the experiment. Our results show a shift in the taxonomic composition of the community over time that is dependent on the nutrient addition regime. Significant differences in the functional potential of the communities were detected, with an interaction between bloom period (pre-bloom, bloom and post-bloom) and nutrient treatment (p = 0.004). A sharp drop in functional similarity was observed in the first week in all treatments and after 20 days had not returned to pre-bloom levels. Changes within energy metabolism pathways showed a remarkable enrichment of the dissimilatory nitrate reduction pathway in the post-bloom period. Eukaryotic oxidative phosphorylation and photosynthetic antenna proteins were more abundant during the bloom, especially in the continuous treatment with silicate. Our results suggest that continuous (i.e. chronic) nutrient enrichment has a larger effect on the functioning of marine systems compared to a single (i.e acute) addition. A deep understanding of the functional and taxonomic shifts in the community during blooms is essential to reverse or mitigate human impacts on coastal environments. HTML XML PDF
      PubDate: Tue, 12 Apr 2022 13:23:41 +030
       
  • 18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National
           Wildlife Refuge, Central Pacific

    • Abstract: Metabarcoding and Metagenomics 6: e78762
      DOI : 10.3897/mbmg.6.78762
      Authors : Brendan N. Reid, Jennifer A. Servis, Molly Timmers, Forest Rohwer, Eugenia Naro-Maciel : To address the global biodiversity crisis, standardized data that are rapidly obtainable through minimally invasive means are needed for documenting change and informing conservation within threatened and diverse systems, such as coral reefs. In this data paper, we describe 18S rRNA gene amplicon data (V1–V3 region) generated from samples collected to begin characterizing coral reef eukaryotic community composition at the Palmyra Atoll National Wildlife Refuge in the Central Pacific Ocean. Sixteen samples were obtained across four sample types: sediments from two sieved fractions (100–500 μm, n = 3; 500 μm-2 mm, n = 3) and sessile material scrapings (n = 3) from Autonomous Reef Monitoring Structures (ARMS) sampled in 2015, as well as seawater from 2012 (n = 7). After filtering and contaminant removal, 3,861 Amplicon Sequence Variants (ASVs) were produced from 1,062,238 reads. The rarefaction curves demonstrated adequate sampling depth, and communities grouped by sample type. The dominant orders across samples were polychaete worms (Eunicida), demosponges (Poecilosclerida), and bryozoans (Cheilostomatida). The ten most common orders in terms of relative abundance comprised ~60% of all sequences and 23% of ASVs, and included reef-building crustose coralline algae (CCA; Corallinophycidae) and stony corals (Scleractinia), two taxa associated with healthy reefs. Highlighting the need for further study, ~21% of the ASVs were identified as uncultured, incertae sedis, or not assigned to phylum or order. This data paper presents the first 18S rDNA survey at Palmyra Atoll and serves as a baseline for biodiversity assessment, monitoring, and conservation of this remote and pristine ecosystem. HTML XML PDF
      PubDate: Tue, 12 Apr 2022 13:23:05 +030
       
  • 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)

    • Abstract: Metabarcoding and Metagenomics 6: e78756
      DOI : 10.3897/mbmg.6.78756
      Authors : Physilia Y. S. Chua, Christian Carøe, Alex Crampton-Platt, Claudia S. Reyes-Avila, Gareth Jones, Daniel G. Streicker, Kristine Bohmann : The feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals they feed on. One DNA-based approach, shotgun sequencing, can be used to obtain such information. Even though it is costly, shotgun sequencing can be used to simultaneously retrieve prey and vampire bat mitochondrial DNA for population studies within one round of sequencing. However, due to the challenges of analysing shotgun sequenced metagenomic data such as false negatives/positives and typically low proportion of reads mapped to diet items, shotgun sequencing has not been used for the identification of prey from common vampire bat blood meals. To overcome these challenges and generate longer mitochondrial contigs which could be useful for prey population studies, we shotgun sequenced common vampire bat blood meal samples (n = 8) and utilised a two-step metagenomic approach based on combining existing bioinformatic workflows (alignment and mtDNA contig assembly) to identify prey. After validating our results from detections made through metabarcoding, we accurately identified the common vampire bats’ prey in six out of eight samples without any false positives. We also generated prey mitochondrial contig lengths between 138 bp to 3231 bp (median = 770 bp, Q1 = 262 bp, Q3 = 1766 bp). This opens the potential to conduct phylogenetic and phylogeographic monitoring of elusive prey species in future studies, through the analyses of blood meal metagenomic data. HTML XML PDF
      PubDate: Thu, 7 Apr 2022 10:00:13 +0300
       
  • Metagenomic insights to the functional potential of sediment microbial
           communities in freshwater lakes

    • Abstract: Metabarcoding and Metagenomics 6: e79265
      DOI : 10.3897/mbmg.6.79265
      Authors : Laura Biessy, John K. Pearman, Sean Waters, Marcus J. Vandergoes, Susanna A. Wood : Molecular-based techniques offer considerable potential to provide new insights into the impact of anthropogenic stressors on lake ecosystems. Microbial communities are involved in many geochemical cycling processes in lakes and a greater understanding of their functions could assist in guiding more targeted remedial actions. Recent advances in metagenomics now make it possible to determine the functional potential of entire microbial communities. The present study investigated microbial communities and their functional potential in surface sediments collected from three lakes with differing trophic states and characteristics. Surface sediments were analysed for their nutrient and elemental contents and metagenomics and metabarcoding analysis undertaken. The nutrients content of the surface sediments did not show as distinct a gradient as water chemistry monitoring data, likely reflecting effects of other lake characteristics, in particular, depth. Metabarcoding and metagenomics revealed differing bacterial community composition and functional potential amongst lakes. Amongst the differentially abundant metabolic pathways, the most prominent were clusters in the energy and xenobiotics pathways. Differences in the energy metabolism paths of photosynthesis and oxidative phosphorylation were observed. These were most likely related to changes in the community composition and especially the presence of cyanobacteria in two of the three lakes. Xenobiotic pathways, such as those involving polycyclic aromatic hydrocarbons, were highest in the lakes with the greatest agricultural land-use in their catchment. These results highlight how microbial metagenomics can be used to gain insights into the causes of differences in trophic status amongst lakes. HTML XML PDF
      PubDate: Fri, 25 Mar 2022 14:57:33 +020
       
  • Annual dynamics of eukaryotic and bacterial communities revealed by 18S
           and 16S rRNA metabarcoding in the coastal ecosystem of Sagami Bay, Japan

    • Abstract: Metabarcoding and Metagenomics 6: e78181
      DOI : 10.3897/mbmg.6.78181
      Authors : Sayaka Sogawa, Kenji Tsuchiya, Satoshi Nagai, Shinji Shimode, Victor S. Kuwahara : 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, forming a dynamic ecosystem. The aim of the present study was to investigate eukaryotic and bacterial communities in the coastal waters of Sagami Bay, using 16S rRNA and 18S rRNA sequencing and to assess the seasonal and vertical dynamics in relation to physicochemical and biological conditions. Eukaryotic and bacterial communities showed synchronous seasonal and vertical changes along with environmental variability. Diversity of plankton community suspended in the surface was lower than those at the subsurface layers in both the eukaryotes and bacteria communities; however, community diversity showed different characteristics in the subsurface where the eukaryotic community at the deeper layer (100 m) was as low as the surface and highest in intermediate depth layers (10–50 m), while that of bacterial community was highest in the deeper layer (100 m). The annual variability of the coastal microbial communities was driven, not only by the seasonal changes of abiotic and biotic factors and short-term rapid changes by river water inflow and phytoplankton blooms, but also largely influenced by deep-seawater upwellings due to the unique seafloor topography. HTML XML PDF
      PubDate: Mon, 28 Feb 2022 10:05:31 +020
       
  • Comparing PCR-generated artifacts of different polymerases for improved
           accuracy of DNA metabarcoding

    • Abstract: Metabarcoding and Metagenomics 6: e77704
      DOI : 10.3897/mbmg.6.77704
      Authors : Satoshi Nagai, Sirje Sildever, Noriko Nishi, Satoshi Tazawa, Leila Basti, Takanori Kobayashi, Yoshizumi Ishino : Accuracy of PCR amplification is vital for obtaining reliable amplicon-sequencing results by metabarcoding. Here, we performed a comparative analysis of error profiles in the PCR products by 14 different PCR kits using a mock eukaryotic community DNA sample mimicking metabarcoding analysis. To prepare a mock eukaryotic community from the marine environment, equal amounts of plasmid DNA from 40 microalgal species were mixed and used for amplicon-sequencing by a high-throughput sequencing approach. To compare the differences in PCR kits used for this experiment, we focused on the following seven parameters: 1) Quality, 2) Chimera, 3) Blast top hit accuracy, 4) Deletion, 5) Insertion, 6) Base substitution and 7) Amplification bias amongst species. The results showed statistically significant differences (p < 0.05) for all of the seven parameters depending on the PCR kits used. These differences may result from the different DNA polymerases included in each kit, although the result can also be influenced by PCR reaction conditions. Simultaneous analysis of several parameters suggested that kits containing KOD plus Neo (TOYOBO) and HotStart Taq DNA polymerase (BiONEER, CA, US) at the annealing temperature of 65 °C displayed better results in terms of parameters associated with chimeras, top hit similarity and deletions. HTML XML PDF
      PubDate: Mon, 21 Feb 2022 11:33:29 +020
       
  • Development and evaluation of PCR primers for environmental DNA (eDNA)
           metabarcoding of Amphibia

    • Abstract: Metabarcoding and Metagenomics 6: e76534
      DOI : 10.3897/mbmg.6.76534
      Authors : Masayuki K. Sakata, Mone U. Kawata, Atsushi Kurabayashi, Takaki Kurita, Masatoshi Nakamura, Tomoyasu Shirako, Ryosuke Kakehashi, Kanto Nishikawa, Mohamad Yazid Hossman, Takashi Nishijima, Junichi Kabamoto, Masaki Miya, Toshifumi Minamoto : Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians’ ecological traits (e.g. nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding – analysis of extra-organismal DNA released into the environment – allows the easy and effective monitoring of the biodiversity of aquatic organisms. Here, we developed and tested the utility of original PCR primer sets. First, we conducted in vitro PCR amplification tests with universal primer candidates using total DNA extracted from amphibian tissues. Five primer sets successfully amplified the target DNA fragments (partial 16S rRNA gene fragments of 160–311 bp) from all 16 taxa tested (from the three living amphibian orders Anura, Caudata and Gymnophiona). Next, we investigated the taxonomic resolution retrieved using each primer set. The results revealed that the universal primer set “Amph16S” had the highest resolution amongst the tested sets. Finally, we applied Amph16S to the water samples collected in the field and evaluated its detection capability by comparing the species detected using eDNA and physical survey (capture-based sampling and visual survey) in multiple agricultural ecosystems across Japan (160 sites in 10 areas). The eDNA metabarcoding with Amph16S detected twice as many species as the physical surveys (16 vs. 8 species, respectively), indicating the effectiveness of Amph16S in biodiversity monitoring and ecological research for amphibian communities. HTML XML PDF
      PubDate: Mon, 21 Feb 2022 08:59:01 +020
       
  • Shifts in DNA yield and biological community composition in stored
           sediment: implications for paleogenomic studies

    • Abstract: Metabarcoding and Metagenomics 6: e78128
      DOI : 10.3897/mbmg.6.78128
      Authors : Katie A. Brasell, Xavier Pochon, Jamie Howarth, John K. Pearman, Anastasija Zaiko, Lucy Thompson, Marcus J. Vandergoes, Kevin S. Simon, Susanna A. Wood : Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies. HTML XML PDF
      PubDate: Tue, 1 Feb 2022 10:01:36 +0200
       
  • Comparing species detection success between molecular markers in DNA
           metabarcoding of coastal macroinvertebrates

    • Abstract: Metabarcoding and Metagenomics 5: e70063
      DOI : 10.3897/mbmg.5.70063
      Authors : Barbara R. Leite, Pedro E. Vieira, Jesús S. Troncoso, Filipe O. Costa : DNA metabarcoding has great potential to improve marine biomonitoring programs by providing a rapid and accurate assessment of species composition in zoobenthic communities. However, some methodological improvements are still required, especially regarding failed detections, primers efficiency and incompleteness of databases. Here we assessed the efficiency of two different marker loci (COI and 18S) and three primer pairs in marine species detection through DNA metabarcoding of the macrozoobenthic communities colonizing three types of artificial substrates (slate, PVC and granite), sampled between 3 and 15 months of deployment. To accurately compare detection success between markers, we also compared the representativeness of the detected species in public databases and revised the reliability of the taxonomic assignments. Globally, we recorded extensive complementarity in the species detected by each marker, with 69% of the species exclusively detected by either 18S or COI. Individually, each of the three primer pairs recovered, at most, 52% of all species detected on the samples, showing also different abilities to amplify specific taxonomic groups. Most of the detected species have reliable reference sequences in their respective databases (82% for COI and 72% for 18S), meaning that when a species was detected by one marker and not by the other, it was most likely due to faulty amplification, and not by lack of matching sequences in the database. Overall, results showed the impact of marker and primer applied on species detection ability and indicated that, currently, if only a single marker or primer pair is employed in marine zoobenthos metabarcoding, a fair portion of the diversity may be overlooked. HTML XML PDF
      PubDate: Wed, 29 Dec 2021 17:51:59 +020
       
  • Towards harmonization of DNA metabarcoding for monitoring marine
           macrobenthos: the effect of technical replicates and pooled DNA
           extractions on species detection

    • Abstract: Metabarcoding and Metagenomics 5: e71107
      DOI : 10.3897/mbmg.5.71107
      Authors : Laure Van den Bulcke, Annelies De Backer, Bart Ampe, Sara Maes, Jan Wittoeck, Willem Waegeman, Kris Hostens, Sofie Derycke : DNA-based monitoring methods are potentially faster and cheaper compared to traditional morphological benthic identification. DNA metabarcoding involves various methodological choices which can introduce bias leading to a different outcome in biodiversity patterns. Therefore, it is important to harmonize DNA metabarcoding protocols to allow comparison across studies and this requires a good understanding of the effect of methodological choices on diversity estimates. This study investigated the impact of DNA and PCR replicates on the detection of macrobenthos species in locations with high, medium and low diversity. Our results show that two to three DNA replicates were needed in locations with a high and medium diversity to detect at least 80% of the species found in the six DNA replicates, while three to four replicates were needed in the location with low diversity. In contrast to general belief, larger body size or higher abundance of the species in a sample did not increase its detection prevalence among DNA replicates. However, rare species were less consistently detected across all DNA replicates of the location with high diversity compared to locations with less diversity. Our results further show that pooling of DNA replicates did not significantly alter diversity patterns, although a small number of rare species was lost. Finally, our results confirm high variation in species detection between PCR replicates, especially for the detection of rare species. These results contribute to create reliable, time and cost efficient metabarcoding protocols for the characterization of macrobenthos. HTML XML PDF
      PubDate: Wed, 29 Dec 2021 17:50:59 +020
       
  • Using DNA metabarcoding to decipher the diet plant component of mammals
           from the Eastern Mediterranean region

    • Abstract: Metabarcoding and Metagenomics 5: e70107
      DOI : 10.3897/mbmg.5.70107
      Authors : Liliane Boukhdoud, Carole Saliba, Lillian D. Parker, Nancy Rotzel McInerney, Rhea Kahale, Issam Saliba, Jesús E. Maldonado, Magda Bou Dagher Kharrat : 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 necessary for species conservation and persistence, and diet analysis is a prerequisite tool to evaluate these interactions. Understanding these processes is crucial for identifying conservation targets and for executing efficient reforestation and ecological restoration. In this study, we applied a scat DNA metabarcoding technique using the P6-loop of the trnL (UAA) chloroplastic marker to describe the seasonal plant diet composition of 15 mammal species from a highly biodiverse Lebanese forest in the Eastern Mediterranean. We also recovered plant seeds, when present, from the scats for identification. The mammal species belong to 10 families from 5 different orders. More than 133 plant species from 54 plant families were detected and identified. Species from the Rosaceae, Poaceae, Apiaceae, Fabaceae, Fagaceae and Berberidaceae families were consumed by the majority of the mammals and should be taken into consideration in future reforestation and conservation projects. Our results showed that the DNA metabarcoding approach provides a promising method for tracking the dietary plant components of a wide diversity of mammals, yielding key insights into plant-animal interactions inside Lebanon’s forests. HTML XML PDF
      PubDate: Mon, 20 Dec 2021 11:27:29 +020
       
  • Revision and annotation of DNA barcode records for marine invertebrates:
           report of the 8th iBOL conference hackathon

    • Abstract: Metabarcoding and Metagenomics 5: e67862
      DOI : 10.3897/mbmg.5.67862
      Authors : Adriana E. Radulovici, Pedro E. Vieira, Sofia Duarte, Marcos A. L. Teixeira, Luisa M. S. Borges, Bruce E. Deagle, Sanna Majaneva, Niamh Redmond, Jessica A. Schultz, Filipe O. Costa : The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable. HTML XML PDF
      PubDate: Thu, 16 Dec 2021 10:57:43 +020
       
  • Phytool, a ShinyApp to homogenise taxonomy of freshwater microalgae from
           DNA barcodes and microscopic observations

    • Abstract: Metabarcoding and Metagenomics 5: e74096
      DOI : 10.3897/mbmg.5.74096
      Authors : Alexis Canino, Agnès Bouchez, Christophe Laplace-Treyture, Isabelle Domaizon, Frédéric Rimet : Methods for biomonitoring of freshwater phytoplankton are evolving rapidly with eDNA-based methods, offering great complementarity with microscopy. Metabarcoding approaches have been more commonly used over the last years, with a continuous increase in the amount of data generated. Depending on the researchers and the way they assigned barcodes to species (bioinformatic pipelines and molecular reference databases), the taxonomic assignment obtained for HTS DNA reads might vary. This is also true for traditional taxonomic studies by microscopy with regular adjustments of the classification and taxonomy. For those reasons (leading to non-homogeneous taxonomies), gap-analyses and comparisons between studies become even more challenging and the curation processes to find potential consensus names are time-consuming. Here, we present a web-based application (Phytool), developed with ShinyApp (Rstudio), that aims to make the harmonisation of taxonomy easier and in a more efficient way, using a complete and up-to-date taxonomy reference database for freshwater microalgae. Phytool allows users to homogenise and update freshwater phytoplankton taxonomical names from sequence files and data tables directly uploaded in the application. It also gathers barcodes from curated references in a user-friendly way in which it is possible to search for specific organisms. All the data provided are downloadable with the possibility to apply filters in order to select only the required taxa and fields (e.g. specific taxonomic ranks). The main goal is to make accessible to a broad range of users the connection between microscopy and molecular biology and taxonomy through different ready-to-use functions. This study estimates that only 25% of species of freshwater phytoplankton in Phytobs are associated with a barcode. We plead for an increased effort to enrich reference databases by coupling taxonomy and molecular methods. Phytool should make this crucial work more efficient. The application is available at https://caninuzzo.shinyapps.io/phytool_v1/ HTML XML PDF
      PubDate: Wed, 15 Dec 2021 08:44:20 +020
       
  • The Dark mAtteR iNvestigator (DARN) tool: getting to know the known
           unknowns in COI amplicon data

    • Abstract: Metabarcoding and Metagenomics 5: e69657
      DOI : 10.3897/mbmg.5.69657
      Authors : Haris Zafeiropoulos, Laura Gargan, Sanni Hintikka, Christina Pavloudi, Jens Carlsson : The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/and amplicon sequence variants (ASVs) retrieved from such studies do not get a taxonomic assignment with a reference sequence. To assess and investigate such sequences, we have developed the Dark mAtteR iNvestigator (DARN) software tool. For this purpose, a reference COI-oriented phylogenetic tree was built from 1,593 consensus sequences covering all the three domains of life. With respect to eukaryotes, consensus sequences at the family level were constructed from 183,330 sequences retrieved from the Midori reference 2 database, which represented 70% of the initial number of reference sequences. Similarly, sequences from 431 bacterial and 15 archaeal taxa at the family level (29% and 1% of the initial number of reference sequences respectively) were retrieved from the BOLD and the PFam databases. DARN makes use of this phylogenetic tree to investigate COI pre-processed sequences of amplicon samples to provide both a tabular and a graphical overview of their phylogenetic assignments. To evaluate DARN, both environmental and bulk metabarcoding samples from different aquatic environments using various primer sets were analysed. We demonstrate that a large proportion of non-target prokaryotic organisms, such as bacteria and archaea, are also amplified in eDNA samples and we suggest prokaryotic COI sequences to be included in the reference databases used for the taxonomy assignment to allow for further analyses of dark matter. DARN source code is available on GitHub at https://github.com/hariszaf/darn and as a Docker image at https://hub.docker.com/r/hariszaf/darn. HTML XML PDF
      PubDate: Wed, 3 Nov 2021 16:00:22 +0200
       
  • Plankton biodiversity and species co-occurrence based on environmental DNA
           – a multiple marker study

    • Abstract: Metabarcoding and Metagenomics 5: e72371
      DOI : 10.3897/mbmg.5.72371
      Authors : Sirje Sildever, Peeter Laas, Natalja Kolesova, Inga Lips, Urmas Lips, Satoshi Nagai : Metabarcoding in combination with high-throughput sequencing (HTS) allows simultaneous detection of multiple taxa by targeting single or several taxonomically informative gene regions from environmental DNA samples. In this study, a multiple-marker HTS approach was applied to investigate the plankton diversity and seasonal succession in the Baltic Sea from winter to autumn. Four different markers targeting the 16S, 18S, and 28S ribosomal RNA genes were employed, including a marker for more efficient dinoflagellate detection. Typical seasonal changes were observed in phyto- and bacterioplankton communities. In phytoplankton, the appearance patterns of selected common, dominant, or harmful species followed the patterns also confirmed based on 20 years of phytoplankton monitoring data. In the case of zooplankton, both macro- and microzooplankton species were detected. However, no seasonal patterns were detected in their appearance. In total, 15 and 2 new zoo- and phytoplankton species were detected from the Baltic Sea. HTS approach was especially useful for detecting microzooplankton species as well as for investigating the co-occurrence and potential interactions of different taxa. The results of this study further exemplify the efficiency of metabarcoding for biodiversity monitoring and the advantage of employing multiple markers through the detection of species not identifiable based on a single marker survey and/or by traditional morphology-based methods. HTML XML PDF
      PubDate: Wed, 3 Nov 2021 13:48:46 +0200
       
  • 18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary,
           New York

    • Abstract: Metabarcoding and Metagenomics 5: e69691
      DOI : 10.3897/mbmg.5.69691
      Authors : Melissa R. Ingala, Irena E. Werner, Allison M. Fitzgerald, Eugenia Naro-Maciel : Characterising and monitoring biological diversity to foster sustainable ecosystems is highly recommended as urban centres rapidly expand. However, much of New York City’s biodiversity remains undescribed, including in the historically degraded, but recovering Bronx River Estuary. In a pilot study to identify organisms and characterise biodiversity patterns there, 18S rRNA gene amplicons (V1–V3 region), obtained from river sediments and surface waters of Hunts Point Riverside and Soundview Parks, were sequenced. Across 48 environmental samples collected over three seasons in 2015 and 2016, following quality control and contaminant removal, 2,763 Amplicon Sequence Variants (ASVs) were identified from 1,918,463 sequences. Rarefaction analysis showed sufficient sampling depth, and community composition varied over time and by substrate at the study sites over the sampling period. Protists, plants, fungi and animals, including organisms of management concern, such as Eastern oysters (Crassostrea virginica), wildlife pathogens and groups related to Harmful Algal Blooms, were detected. The most common taxa identified in river sediments were annelid worms, nematodes and diatoms. In the water column, the most commonly observed organisms were diatoms, algae of the phylum Cryptophyceae, ciliates and dinoflagellates. The presented dataset demonstrates the reach of 18S rRNA metabarcoding for characterising biodiversity in an urban estuary. HTML XML PDF
      PubDate: Tue, 7 Sep 2021 08:22:23 +0300
       
  • Internal transcribed spacer primer evaluation for vascular plant
           metabarcoding

    • Abstract: Metabarcoding and Metagenomics 5: e68155
      DOI : 10.3897/mbmg.5.68155
      Authors : Andreas Kolter, Birgit Gemeinholzer : The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations in metabarcoding of plants, aside from selecting a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavourable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimisation, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that continuous quality assurance is indispensable for reliable metabarcoding results. HTML XML PDF
      PubDate: Thu, 2 Sep 2021 17:46:45 +0300
       
  • Ciliate SSU-rDNA reference alignments and trees for phylogenetic
           placements of metabarcoding data

    • Abstract: Metabarcoding and Metagenomics 5: e69602
      DOI : 10.3897/mbmg.5.69602
      Authors : Ľubomír Rajter, Micah Dunthorn : Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements. HTML XML PDF
      PubDate: Mon, 30 Aug 2021 16:48:26 +030
       
  • How can integrated morphotaxonomy- and metabarcoding-based diatom
           assemblage analyses best contribute to the ecological assessment of
           streams'

    • Abstract: Metabarcoding and Metagenomics 5: e68438
      DOI : 10.3897/mbmg.5.68438
      Authors : Panayiota Pissaridou, Marco Cantonati, Agnes Bouchez, Iakovos Tziortzis, Gerald Dörflinger, Marlen I. Vasquez : Environmental conditions, such as nutrient concentrations, salinity, elevation etc., shape diatom assemblages of periphytic biofilms. These assemblages respond rapidly to environmental changes, a fact which makes diatoms valuable bioindicators. Hence, freshwater biomonitoring programmes currently use diatom indices (e.g. EU Water Framework Directive - WFD). To date, microscopy-based assessments require high taxonomic expertise for diatom identification at the species level. High-throughput technologies now provide cost-effective identification approaches that are promising, complementary or alternative tools for bioassessment. The suitability of the metabarcoding method is evaluated for the first time in the Cyprus streams WFD monitoring network, an eastern Mediterranean country with many endemic species and results are compared to the results acquired from the morphotaxonomic analysis. Morphotaxonomic identification was conducted microscopically, using the most updated taxonomic concepts, literature and online resources. At the same time, DNA metabarcoding involved the use of the rbcL 312 bp barcode, high-throughput sequencing and bioinformatic analysis. The ecological status was calculated using the IPS Index. Results show a positive correlation between morpho-taxonomic and molecular IPS scores. Discrepancies between the two methodologies are related to the limitations of both techniques. This study confirmed that Fistulifera saprophila can have a crucial role in key differences observed, as it negatively influences IPS scores and microscopy methods frequently overlook it. Importantly, gaps in the DNA barcoding reference databases lead to a positive overestimation in IPS scores. Overall, we conclude that DNA metabarcoding offsets the morphotaxonomic methodology for the ecological quality assessment of freshwaters. HTML XML PDF
      PubDate: Wed, 25 Aug 2021 14:32:09 +030
       
  • The power of metabarcoding: Can we improve bioassessment and biodiversity
           surveys of stream macroinvertebrate communities'

    • Abstract: Metabarcoding and Metagenomics 5: e68938
      DOI : 10.3897/mbmg.5.68938
      Authors : Jarno Turunen, Heikki Mykrä, Vasco Elbrecht, Dirk Steinke, Thomas Braukmann, Jukka Aroviita : Most stream bioassessment and biodiversity surveys are currently based on morphological identification of communities. However, DNA metabarcoding is emerging as a fast and cost-effective alternative for species identification. We compared both methods in a survey of benthic macroinvertebrate communities across 36 stream sites in northern Finland. We identified 291 taxa of which 62% were identified only by DNA metabarcoding. DNA metabarcoding produced extensive species level inventories for groups (Oligochaeta, Chironomidae, Simuliidae, Limoniidae and Limnephilidae), for which morphological identification was not feasible due to the high level of expertise needed. Metabarcoding also provided more insightful taxonomic information on the occurrence of three red-listed vulnerable or data deficient species, the discovery of two likely cryptic and potentially new species to Finland and species information of insect genera at an early larval stage that could not be separated morphologically. However, it systematically failed to reliably detect the occurrence of gastropods that were easily identified morphologically. The impact of mining on community structure could only be shown using DNA metabarcoding data which suggests that the finer taxonomic detail can improve detection of subtle impacts. Both methods generally exhibited similar strength of community-environment relationships, but DNA metabarcoding showed better performance with presence/absence data than with relative DNA sequence abundances. Our results suggest that DNA metabarcoding holds a promise for future anthropogenic impact assessments, although, in our case, the performance did not improve much from the morphological species identification. The key advantage of DNA metabarcoding lies in efficient biodiversity surveys, taxonomical studies and applications in conservation biology. HTML XML PDF
      PubDate: Wed, 28 Jul 2021 09:47:42 +030
       
  • Evaluating the performance of DNA metabarcoding for assessment of
           zooplankton communities in Western Lake Superior using multiple markers

    • Abstract: Metabarcoding and Metagenomics 5: e64735
      DOI : 10.3897/mbmg.5.64735
      Authors : Christy Meredith, Joel Hoffman, Anett Trebitz, Erik Pilgrim, Sarah Okum, John Martinson, Ellen S. Cameron : For DNA metabarcoding to attain its potential as a community assessment tool, we need to better understand its performance versus traditional morphological identification and work to address any remaining performance gaps in incorporating DNA metabarcoding into community assessments. Using fragments of the 18S nuclear and 16S mitochondrial rRNA genes and two fragments of the mitochondrial COI marker, we examined the use of DNA metabarcoding and traditional morphological identification for understanding the diversity and composition of crustacean zooplankton at 42 sites across western Lake Superior. We identified 51 zooplankton taxa (genus or species, depending on the finest resolution of the taxon across all identification methods), of which 17 were identified using only morphological traits, 13 using only DNA and 21 using both methods. The taxa found using only DNA metabarcoding included four species and one genus-level identification not previously known to occur in Lake Superior, the presence of which still needs to be confirmed. A substantial portion of taxa that were identified to genus or species by morphological identification, but not identified using DNA metabarcoding, had zero (“no record”) or < 2 (“underrepresented records”) reference barcodes in the BOLD or NCBI databases (63% for COI, 80% for 16S, 74% for 18S). The two COI marker fragments identified the most genus- and species-level taxa, whereas 18S was the only marker whose family-level percent sequence abundance patterns showed high correlation to composition patterns from morphological identification, based on a NMDS analysis of Bray-Curtis similarities. Multiple replicates were collected at a subset of sites and an occupancy analysis was performed, which indicated that rare taxa were more likely to be detected using DNA metabarcoding than traditional morphology. Our results support that DNA metabarcoding can augment morphological identification for estimating zooplankton diversity and composition of zooplankton over space and time, but may require use of multiple markers. Further addition of taxa to reference DNA databases will improve our ability to use DNA metabarcoding to identify zooplankton and other invertebrates in aquatic surveys. HTML XML PDF
      PubDate: Wed, 21 Jul 2021 19:17:52 +030
       
  • Wet grinding of invertebrate bulk samples – a scalable and
           cost-efficient protocol for metabarcoding and metagenomics

    • Abstract: Metabarcoding and Metagenomics 5: e67533
      DOI : 10.3897/mbmg.5.67533
      Authors : Dominik Buchner, Peter Haase, Florian Leese : Most metabarcoding protocols for invertebrate bulk samples start with sample homogenisation, followed by DNA extraction, amplification of a specific marker region, and sequencing. Many of the above-mentioned laboratory steps have been verified thoroughly and best practice strategies exist, yet, no clear recommendation for the basis of almost all metabarcoding studies exists: the homogenisation of samples itself. Two different categories of devices are typically used for homogenisation: bead mills or blenders. Both have upsides and downsides. Bead mills rely on single-use plastics and therefore produce a lot of waste and are expensive. In addition to that, processing times can go up to 30 minutes making them unsuitable for large-scale studies. Blenders can handle larger sample volumes in a shorter time, and be cleaned – yet suffer from an increased risk of cross-contamination. We aimed to develop a fast, robust, cheap, and reliable sample homogenisation protocol that overcomes limitations of both approaches, i.e. does not produce difficult to discard waste and avoid single-use plastics while reducing overall costs. We tested the performance of the new protocol using six size-sorted Malaise trap samples and six unsorted stream macroinvertebrate kick-net samples. We used 14 replicates per sample and included many negative controls at different steps of the protocol to quantify the impacts of i) insufficient homogenisation and ii) cross-contamination. Our results show that 3-min homogenisation is sufficient to recover about 80% of OTUs per sample in each replicate and that a non-hazardous DIY cleaning solution provides an effective and efficient way of cleaning. The improvements of the protocol in terms of speed, ease of handling, an overall reduction of costs as well as the documented reliability and robustness make it an important candidate for sample homogenisation after sampling in particular for large-scale and regulatory metabarcoding but also metagenomics biodiversity assessments and monitoring. HTML XML PDF
      PubDate: Tue, 20 Jul 2021 13:27:58 +030
       
  • Beyond fish eDNA metabarcoding: Field replicates disproportionately
           improve the detection of stream associated vertebrate species

    • Abstract: Metabarcoding and Metagenomics 5: e66557
      DOI : 10.3897/mbmg.5.66557
      Authors : Till-Hendrik Macher, Robin Schütz, Jens Arle, Arne J. Beermann, Jan Koschorreck, Florian Leese : Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale. HTML XML PDF
      PubDate: Tue, 13 Jul 2021 11:59:20 +030
       
  • Potential for cross-contamination of diatom DNA samples when using
           toothbrushes

    • Abstract: Metabarcoding and Metagenomics 5: e66503
      DOI : 10.3897/mbmg.5.66503
      Authors : Martyn G. Kelly, Tim Jones, Kerry Walsh : 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 analysis by light microscopy. This paper looks at the scale of contamination encountered when this technique is used to sample diatoms for metabarcoding analyses, as well as at the scale of contamination to be expected if stream, rather than distilled water, is used to wash diatoms from stones. Although some contamination attributable to toothbrushes was detected, read numbers were low and had no effect on index calculation or ecological status estimates. However, if the primary focus of a study is to thoroughly document diversity in a sample, then even this small level of contamination may be unacceptable and more stringent measures may be required. HTML XML PDF
      PubDate: Mon, 17 May 2021 15:26:59 +030
       
  • Effects of Malaise trap spacing on species richness and composition of
           terrestrial arthropod bulk samples

    • Abstract: Metabarcoding and Metagenomics 5: e59201
      DOI : 10.3897/mbmg.5.59201
      Authors : Dirk Steinke, Thomas WA Braukmann, Laura Manerus, Allan Woodhouse, Vasco Elbrecht : The Malaise trap is a popular device for assessing diverse terrestrial arthropod communities because it collects large samples with modest effort. A number of factors influence its collection efficiency, placement being one of them. For instance, when designing larger biotic surveys using arrays of Malaise traps we need to know the optimal distance between individual traps that maximises observable species richness and community composition. We examined the influence of spacing between Malaise traps by metabarcoding samples from two field experiments at a site in Waterloo, Ontario, Canada. For one experiment, we used two trap pairs deployed at weekly increasing distances (3 m increments from 3 to 30 m). The second experiment involved a total of 10 traps set up in a row at 3 m distance intervals for three consecutive weeks. Results show that community similarity of samples decreases over distance between traps. The amount of species shared between trap pairs drops considerably at about 18 m trap-to-trap distance. This change can be observed across all major taxonomic groups and for two different habitat types (grassland and forest). Large numbers of OTUs found only once within samples cause rather large dissimilarity between distance pairs even at close proximity. This could be caused by a large number of transient species from adjacent habitats which arrive at the trap through passive transport, as well as capture of rare taxa, which end up in different traps by chance. HTML XML PDF
      PubDate: Fri, 9 Apr 2021 10:53:49 +0300
       
  • Metabarcoding of environmental samples suggest wide distribution of
           eelgrass (Zostera marina) pathogens in the north Pacific

    • Abstract: Metabarcoding and Metagenomics 5: e62823
      DOI : 10.3897/mbmg.5.62823
      Authors : Damian M. Menning, Hunter A. Gravley, Melissa N. Cady, Daniel Pepin, Sandy Wyllie-Echeverria, David H. Ward, Sandra L. Talbot : Seagrass meadows provide important ecological services to the marine environment but are declining worldwide. Although eelgrass meadows in the north Pacific are thought to be relatively healthy, few studies have assessed the presence of known disease pathogens in these meadows. In a pilot study to test the efficacy of the methods and to provide foundational disease biodiversity data in the north Pacific, we leveraged metabarcoding of environmental DNA extracted from water, sediment, and eelgrass tissue samples collected from five widely distributed eelgrass meadows in Alaska and one in Japan and uncovered wide prevalence of two classes of pathogenic organisms – Labyrinthula zosterae and other associated strains of Labyrinthula, and the Phytophthora/Halophytophthora blight species complex – known to have caused decline in eelgrass (Zostera marina) elsewhere in the species’ global distribution. Although the distribution of these disease organisms is not well understood in the north Pacific, we uncovered the presence of at least one eelgrass pathogen at every locality sampled. HTML XML PDF
      PubDate: Fri, 9 Apr 2021 08:19:12 +0300
       
  • Metadata standards and practical guidelines for specimen and DNA curation
           when building barcode reference libraries for aquatic life

    • Abstract: Metabarcoding and Metagenomics 5: e58056
      DOI : 10.3897/mbmg.5.58056
      Authors : Frédéric Rimet, Eva Aylagas, Angel Borja, Agnès Bouchez, Alexis Canino, Christian Chauvin, Teofana Chonova, Fedor Ciampor Jr, Filipe О. Costa, Benoit J. D. Ferrari, Romain Gastineau, Chloé Goulon, Muriel Gugger, Maria Holzmann, Regine Jahn, Maria Kahlert, Wolf-Henning Kusber, Christophe Laplace-Treyture, Florian Leese, Frederik Leliaert, David G. Mann, Frédéric Marchand, Vona Méléder, Jan Pawlowski, Serena Rasconi, Sinziana Rivera, Rodolphe Rougerie, Magali Schweizer, Rosa Trobajo, Valentin Vasselon, Régis Vivien, Alexander Weigand, Andrzej Witkowski, Jonas Zimmermann, Torbjørn Ekrem : DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data. HTML XML PDF
      PubDate: Fri, 26 Feb 2021 09:00:07 +020
       
  • Application of propylene glycol in DNA-based studies of invertebrates

    • Abstract: Metabarcoding and Metagenomics 5: e57278
      DOI : 10.3897/mbmg.5.57278
      Authors : Alexander M. Weigand, Noah Desquiotz, Hannah Weigand, Nikolaus Szucsich : High-throughput sequencing (HTS) studies on invertebrates commonly use ethanol as the main sample fixative (upon collection) and preservative (for storage and curation). However, alternative agents exists, which should not be automatically neglected when studies are newly designed. This review provides an overview of the application of propylene glycol (PG) in DNA-based studies of invertebrates, thus to stimulate an evidence-based discussion. The use of PG in DNA-based studies of invertebrates is still limited (n = 79), but a steady increase has been visible since 2011. Most studies used PG as a fixative for passive trapping (73%) and performed Sanger sequencing (66%; e.g. DNA barcoding). More recently, HTS setups joined the field (11%). Terrestrial Coleoptera (30%) and Diptera (20%) were the most studied groups. Very often, information on the grade of PG used (75%) or storage conditions (duration, temperature) were lacking. This rendered direct comparisons of study results difficult, and highlight the need for further systematic studies on these subjects. When compared to absolute ethanol, PG can be more widely and cheaply acquired (e.g. as an antifreeze, 13% of studies). It also enables longer trapping intervals, being especially relevant at remote or hard-to-reach places. Shipping of PG-conserved samples is regarded as risk-free and is authorised, pinpointing its potential for larger trapping programs or citizen science projects. Its property to retain flexibility of morphological characters as well as to lead to a reduced shrinkage effect was especially appraised by integrative study designs. Finally, the so far limited application of PG in the context of HTS showed promising results for short read amplicon sequencing and reduced representation methods. Knowledge of the influence of PG fixation and storage for long(er) read HTS setups is currently unavailable. Given our review results and taking difficulties of direct methodological comparisons into account, future DNA-based studies of invertebrates should on a case-by-case basis critically scrutinise if the application of PG in their anticipated study design can be of benefit. HTML XML PDF
      PubDate: Mon, 4 Jan 2021 15:31:58 +0200
       
 
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