201
|
Thompson LR, Anderson SR, Den Uyl PA, Patin NV, Lim SJ, Sanderson G, Goodwin KD. Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake. Gigascience 2022; 11:6651346. [PMID: 35902092 PMCID: PMC9334028 DOI: 10.1093/gigascience/giac066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/28/2022] [Accepted: 06/15/2022] [Indexed: 12/21/2022] Open
Abstract
Background Amplicon sequencing (metabarcoding) is a common method to survey diversity of environmental communities whereby a single genetic locus is amplified and sequenced from the DNA of whole or partial organisms, organismal traces (e.g., skin, mucus, feces), or microbes in an environmental sample. Several software packages exist for analyzing amplicon data, among which QIIME 2 has emerged as a popular option because of its broad functionality, plugin architecture, provenance tracking, and interactive visualizations. However, each new analysis requires the user to keep track of input and output file names, parameters, and commands; this lack of automation and standardization is inefficient and creates barriers to meta-analysis and sharing of results. Findings We developed Tourmaline, a Python-based workflow that implements QIIME 2 and is built using the Snakemake workflow management system. Starting from a configuration file that defines parameters and input files—a reference database, a sample metadata file, and a manifest or archive of FASTQ sequences—it uses QIIME 2 to run either the DADA2 or Deblur denoising algorithm; assigns taxonomy to the resulting representative sequences; performs analyses of taxonomic, alpha, and beta diversity; and generates an HTML report summarizing and linking to the output files. Features include support for multiple cores, automatic determination of trimming parameters using quality scores, representative sequence filtering (taxonomy, length, abundance, prevalence, or ID), support for multiple taxonomic classification and sequence alignment methods, outlier detection, and automated initialization of a new analysis using previous settings. The workflow runs natively on Linux and macOS or via a Docker container. We ran Tourmaline on a 16S ribosomal RNA amplicon data set from Lake Erie surface water, showing its utility for parameter optimization and the ability to easily view interactive visualizations through the HTML report, QIIME 2 viewer, and R- and Python-based Jupyter notebooks. Conclusion Automated workflows like Tourmaline enable rapid analysis of environmental amplicon data, decreasing the time from data generation to actionable results. Tourmaline is available for download at github.com/aomlomics/tourmaline.
Collapse
Affiliation(s)
- Luke R Thompson
- Northern Gulf Institute, Mississippi State University, Mississippi State, MS 39762, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
| | - Sean R Anderson
- Northern Gulf Institute, Mississippi State University, Mississippi State, MS 39762, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
| | - Paul A Den Uyl
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI 48108, USA
| | - Nastassia V Patin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA.,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Shen Jean Lim
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA.,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Grant Sanderson
- Marine Science Department, University of Hawaii, Hilo, HI 96720, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
| |
Collapse
|
202
|
Hajibabaei M. Demystifying eDNA validation. Trends Ecol Evol 2022; 37:826-828. [PMID: 35902292 DOI: 10.1016/j.tree.2022.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022]
Abstract
As environmental DNA (eDNA) approaches gain momentum for biodiversity analysis, validation becomes a key consideration. I focus on four facets of eDNA validation. Validation through technical processes, legal use, official statements, and 'good enough' scenarios can advance the field to aid societal issues such as climate emergency and biodiversity crisis.
Collapse
Affiliation(s)
- Mehrdad Hajibabaei
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1; Centre for Environmental Genomics Applications, eDNAtec Inc., 14 International Place Unit 103, St. John's, NL, Canada A1A 0R6.
| |
Collapse
|
203
|
Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B. The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The worldwide rapid declines in insect and plant abundance and diversity that have occurred in the past decades have gained public attention and demand for political actions to counteract these declines are growing. Rapid large-scale biomonitoring can aid in observing these changes and provide information for decisions for land management and species protection. Malaise traps have long been used for insect sampling and when insects are captured in these traps, they carry traces of plants they have visited on the body surface or as digested food material in the gut contents. Metabarcoding offers a promising method for identifying these plant traces, providing insight into the plants with which insects are directly interacting at a given time. To test the efficacy of DNA metabarcoding with these sample types, 79 samples from 21 sites across Germany were analysed with the ITS2 barcode. This study, to our knowledge, is the first examination of metabarcoding plant DNA traces from Malaise trap samples. Here, we report on the feasibility of sequencing these sample types, analysis of the resulting taxa, the usage of cultivated plants by insects near nature conservancy areas and the detection of rare and neophyte species. Due to the frequency of contamination and false positive reads, isolation and PCR negative controls should be used in every reaction. Metabarcoding has advantages in efficiency and resolution over microscopic identification of pollen and is the only possible identification method for the other plant traces from Malaise traps and could provide a broad utility for future studies of plant-insect interactions.
Collapse
|
204
|
SIMONS ARIELLEVI, CALDWELL STEVIE, FU MICHELLE, GALLEGOS JOSE, GATHERU MICHAEL, RICCARDELLI LAURA, TRUONG NHI, VIERA VALERIA. Constructing ecological indices for urban environments using species distribution models. Urban Ecosyst 2022. [DOI: 10.1007/s11252-022-01265-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
AbstractIn an increasingly urbanized world, there is a need to study urban areas as their own class of ecosystems as well as assess the impacts of anthropogenic impacts on biodiversity. However, collecting a sufficient number of species observations to estimate patterns of biodiversity in a city can be costly. Here we investigated the use of community science-based data on species occurrences, combined with species distribution models (SDMs), built using MaxEnt and remotely-sensed measures of the environment, to predict the distribution of a number of species across the urban environment of Los Angeles. By selecting species with the most accurate SDMs, and then summarizing these by class, we were able to produce two species richness models (SRMs) to predict biodiversity patterns for species in the class Aves and Magnoliopsida and how they respond to a variety of natural and anthropogenic environmental gradients.We found that species considered native to Los Angeles tend to have significantly more accurate SDMs than their non-native counterparts. For all species considered in this study we found environmental variables describing anthropogenic activities, such as housing density and alterations to land cover, tend to be more influential than natural factors, such as terrain and proximity to freshwater, in shaping SDMs. Using a random forest model we found our SRMs could account for approximately 54% and 62% of the predicted variation in species richness for species in the classes Aves and Magnoliopsida respectively. Using community science-based species occurrences, SRMs can be used to model patterns of urban biodiversity and assess the roles of environmental factors in shaping them.
Collapse
|
205
|
Seeber PA, Epp LS. Environmental
DNA
and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems. Mamm Rev 2022. [DOI: 10.1111/mam.12302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter A. Seeber
- Limnological Institute University of Konstanz Konstanz Germany
| | - Laura S. Epp
- Limnological Institute University of Konstanz Konstanz Germany
| |
Collapse
|
206
|
Magoga G, Forni G, Brunetti M, Meral A, Spada A, De Biase A, Montagna M. Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins. Database (Oxford) 2022; 2022:baac055. [PMID: 35796594 PMCID: PMC9261288 DOI: 10.1093/database/baac055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/15/2022]
Abstract
DNA metabarcoding is a widespread approach for the molecular identification of organisms. While the associated wet-lab and data processing procedures are well established and highly efficient, the reference databases for taxonomic assignment can be implemented to improve the accuracy of identifications. Insects are among the organisms for which DNA-based identification is most commonly used; yet, a DNA-metabarcoding reference database specifically curated for their species identification using software requiring local databases is lacking. Here, we present COins, a database of 5' region cytochrome c oxidase subunit I sequences (COI-5P) of insects that includes over 532 000 representative sequences of >106 000 species specifically formatted for the QIIME2 software platform. Through a combination of automated and manually curated steps, we developed this database starting from all COI sequences available in the Barcode of Life Data System for insects, focusing on sequences that comply with several standards, including a species-level identification. COins was validated on previously published DNA-metabarcoding sequences data (bulk samples from Malaise traps) and its efficiency compared with other publicly available reference databases (not specific for insects). COins can allow an increase of up to 30% of species-level identifications and thus can represent a valuable resource for the taxonomic assignment of insects' DNA-metabarcoding data, especially when species-level identification is needed https://doi.org/10.6084/m9.figshare.19130465.v1.
Collapse
Affiliation(s)
- Giulia Magoga
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, Milano 20133, Italy
| | - Giobbe Forni
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, Milano 20133, Italy
| | - Matteo Brunetti
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, Milano 20133, Italy
| | - Aycan Meral
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, Milano 20133, Italy
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, Milano 20133, Italy
| | - Alessio De Biase
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Viale dell’Università 32, Rome 00185, Italy
| | - Matteo Montagna
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Via Università 100, Naples 80055, Italy
| |
Collapse
|
207
|
Golpour A, Šmejkal M, Čech M, dos Santos RA, Souza AT, Jůza T, Martínez C, Bartoň D, Vašek M, Draštík V, Kolařík T, Kočvara L, Říha M, Peterka J, Blabolil P. Similarities and Differences in Fish Community Composition Accessed by Electrofishing, Gill Netting, Seining, Trawling, and Water eDNA Metabarcoding in Temperate Reservoirs. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.913279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It is difficult to understand the composition and diversity of biological communities in complex and heterogeneous environments using traditional sampling methods. Recently, developments in environmental DNA metabarcoding have emerged as a powerful, non-invasive method for comprehensive community characterization and biodiversity monitoring in different types of aquatic ecosystems. In this study, water eDNA targeting fish (wf-eDNA) and four traditional fish sampling methods (electrofishing, gill netting, seining, trawling) were compared to evaluate the reliability and efficiency of wf-eDNA (vertebrate mitochondrial 12S ribosomal RNA (rRNA) as an alternative approach to assess the diversity and composition of freshwater fish communities. The results of wf-eDNA showed a consistency between the traditional sampling methods regarding species detection. However, some fish species detected using wf-eDNA assay were not detected using traditional sampling methods and vice versa. Comparison of wf-eDNA and traditional sampling methods revealed spatial homogeneity in fish community composition in all reservoirs. Ordination analysis showed that the wf-eDNA approach covers all traditional sampling methods and occupies an intermediate position. In addition, based on the Shannon diversity index, we found that in one reservoir the wf-eDNA method yielded similar fish community diversity to traditional sampling methods. However, in other reservoirs, the calculated Shannon diversity index of the wf-eDNA method was significantly higher than traditional sampling methods. In general, significant positive correlations were found between the wf-eDNA method and almost all traditional sampling methods. We conclude that wf-eDNA seems to be a reliable and complementary approach for biomonitoring and ecosystem management of freshwater ichthyofauna.
Collapse
|
208
|
Kronenberger JA, Wilcox TM, Mason DH, Franklin TW, McKelvey KS, Young MK, Schwartz MK. eDNAssay: a machine learning tool that accurately predicts qPCR cross-amplification. Mol Ecol Resour 2022; 22:2994-3005. [PMID: 35778862 DOI: 10.1111/1755-0998.13681] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/28/2022]
Abstract
Environmental DNA (eDNA) sampling is a highly sensitive and cost-effective technique for wildlife monitoring, notably through the use of qPCR assays. However, it can be difficult to ensure assay specificity when many closely related species cooccur. In theory, specificity may be assessed in silico by determining whether assay oligonucleotides have enough base-pair mismatches with nontarget sequences to preclude amplification. However, the mismatch qualities required are poorly understood, making in silico assessments difficult and often necessitating extensive in vitro testing-typically the greatest bottleneck in assay development. Increasing the accuracy of in silico assessments would therefore streamline the assay development process. In this study, we paired 10 qPCR assays with 82 synthetic gene fragments for 530 specificity tests using SYBR Green intercalating dye (n = 262) and TaqMan hydrolysis probes (n = 268). Test results were used to train random forest classifiers to predict amplification. The primer-only model (SYBR Green-based) and full-assay model (TaqMan probe-based) were 99.6% and 100% accurate, respectively, in cross-validation. We further assessed model performance using six independent assays not used in model training. In these tests the primer-only model was 92.4% accurate (n = 119) and the full-assay model was 96.5% accurate (n = 144). The high performance achieved by these models makes it possible for eDNA practitioners to more quickly and confidently develop assays specific to the intended target. Practitioners can access the full-assay model via eDNAssay (https://NationalGenomicsCenter.shinyapps.io/eDNAssay), a user-friendly online tool for predicting qPCR cross-amplification.
Collapse
Affiliation(s)
- J A Kronenberger
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - T M Wilcox
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - D H Mason
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - T W Franklin
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - K S McKelvey
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - M K Young
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - M K Schwartz
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| |
Collapse
|
209
|
Flück B, Mathon L, Manel S, Valentini A, Dejean T, Albouy C, Mouillot D, Thuiller W, Murienne J, Brosse S, Pellissier L. Applying convolutional neural networks to speed up environmental DNA annotation in a highly diverse ecosystem. Sci Rep 2022; 12:10247. [PMID: 35715444 PMCID: PMC9205931 DOI: 10.1038/s41598-022-13412-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/24/2022] [Indexed: 01/04/2023] Open
Abstract
High-throughput DNA sequencing is becoming an increasingly important tool to monitor and better understand biodiversity responses to environmental changes in a standardized and reproducible way. Environmental DNA (eDNA) from organisms can be captured in ecosystem samples and sequenced using metabarcoding, but processing large volumes of eDNA data and annotating sequences to recognized taxa remains computationally expensive. Speed and accuracy are two major bottlenecks in this critical step. Here, we evaluated the ability of convolutional neural networks (CNNs) to process short eDNA sequences and associate them with taxonomic labels. Using a unique eDNA data set collected in highly diverse Tropical South America, we compared the speed and accuracy of CNNs with that of a well-known bioinformatic pipeline (OBITools) in processing a small region (60 bp) of the 12S ribosomal DNA targeting freshwater fishes. We found that the taxonomic labels from the CNNs were comparable to those from OBITools, with high correlation levels for the composition of the regional fish fauna. The CNNs enabled the processing of raw fastq files at a rate of approximately 1 million sequences per minute, which was about 150 times faster than with OBITools. Given the good performance of CNNs in the highly diverse ecosystem considered here, the development of more elaborate CNNs promises fast deployment for future biodiversity inventories using eDNA.
Collapse
Affiliation(s)
- Benjamin Flück
- Department of Environmental System Science, ETH Zürich, 8092, Zurich, Switzerland.
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
| | - Laëtitia Mathon
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Stéphanie Manel
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | | | | | - Camille Albouy
- DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro - Agrocampus Ouest, Rue de l'Ile d'Yeu, BP21105, 44311, Nantes Cedex 3, France
| | - David Mouillot
- MARBEC, Univ. Montpellier,CNRS, IRD, Ifremer, Montpellier, France
- Institut Universitaire de France, IUF, 75231, Paris, France
| | - Wilfried Thuiller
- CNRS, LECA, Laboratoire d'Écologie Alpine, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, 38000, Grenoble, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Loïc Pellissier
- Department of Environmental System Science, ETH Zürich, 8092, Zurich, Switzerland.
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
| |
Collapse
|
210
|
Chan AHE, Saralamba N, Saralamba S, Ruangsittichai J, Chaisiri K, Limpanont Y, Charoennitiwat V, Thaenkham U. Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes. Sci Rep 2022; 12:9947. [PMID: 35705676 PMCID: PMC9200835 DOI: 10.1038/s41598-022-14176-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
Next-generation sequencing technologies have accelerated the pace of helminth DNA metabarcoding research, enabling species detection in bulk community samples. However, finding suitable genetic markers with robust species-level resolution and primers targeting a broad species range among parasitic helminths are some of the challenges faced. This study aimed to demonstrate the potential use of the mitochondrial 12S and 16S rRNA genes for parasitic helminth (nematodes, trematodes, cestodes) DNA metabarcoding. To demonstrate the robustness of the 12S and 16S rRNA genes for DNA metabarcoding, we determined the proportion of species successfully recovered using mock helminth communities without environment matrix and mock helminth communities artificially spiked with environmental matrices. The environmental matrices are human fecal material, garden soil, tissue, and pond water. Our results revealed the robustness of the mitochondrial rRNA genes, through the high sensitivity of the 12S rRNA gene, and the effectiveness of the 12S and 16S primers targeting platyhelminths. With the mitochondrial rRNA genes, a broad range of parasitc helminths were successfully detected to the species level. The potential of the mitochondrial rRNA genes for helminth DNA metabarcoding was demonstrated, providing a valuable gateway for future helminth DNA metabarcoding applications like helminth detection and biodiversity studies.
Collapse
Affiliation(s)
- Abigail Hui En Chan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Naowarat Saralamba
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sompob Saralamba
- Mathematical and Economic Modelling (MAEMOD), Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jiraporn Ruangsittichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kittipong Chaisiri
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yanin Limpanont
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Urusa Thaenkham
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| |
Collapse
|
211
|
Development of environmental DNA chip for monitoring the invasive alien fishes in dam reservoirs. LANDSCAPE AND ECOLOGICAL ENGINEERING 2022. [DOI: 10.1007/s11355-022-00513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
212
|
Forsman AM, Savage AE, Hoenig BD, Gaither MR. DNA metabarcoding across disciplines: sequencing our way to greater understanding across scales of biological organization. Integr Comp Biol 2022; 62:191-198. [PMID: 35687001 DOI: 10.1093/icb/icac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
DNA metabarcoding describes the use of targeted DNA (i.e., amplicon) sequencing to identify community constituents from a complex sample containing genetic material from multiple organisms, such as water, soil, gut contents, microbiomes, or biofilms. This molecular approach for characterizing mixed DNA samples relies on the development of "universal primers" that allow for effective amplification of target sequences across a broad range of taxa. Armed with optimized lab protocols and rigorous bioinformatics tools, DNA metabarcoding can produce a wealth of information about the hidden biodiversity of various sample types by probing for organisms' molecular footprints. DNA metabarcoding has received considerable popular press over the last few years because of gut microbiome studies in humans and beyond. However, there are many other applications that are continually integrating molecular biology with other fields of study to address questions that have previously been unanswerable, for both prokaryotic and eukaryotic targets. For example, we can now sample mostly-digested gut contents from virtually any organism to learn about ontogeny and foraging ecology. Water samples collected from different locations can be filtered to extract eDNA (i.e., environmental DNA), revealing the biodiversity of fishes and other taxa targeted by carefully selected primer sets. This universal primer metabarcoding approach has even been extended to looking at diverse gene families within single species, which is particularly useful for complex immune system genetics. The purpose of this SICB symposium was to bring together researchers using DNA metabarcoding approaches to (a) showcase the diversity of applications of this technique for addressing questions spanning ecology, evolution, and physiology, and (b) to spark connections among investigators from different fields that are utilizing similar approaches to facilitate optimization and standardization of metabarcoding methods and analyses. The resulting manuscripts from this symposium represent a great diversity of metabarcoding applications and taxonomic groups of interest.
Collapse
Affiliation(s)
- Anna M Forsman
- Department of Biology, University of Central Florida, Orlando, FL, USA.,Genomics & Bioinformatics Cluster, University of Central Florida, Orlando, FL, USA
| | - Anna E Savage
- Department of Biology, University of Central Florida, Orlando, FL, USA
| | - Brandon D Hoenig
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michelle R Gaither
- Department of Biology, University of Central Florida, Orlando, FL, USA.,Genomics & Bioinformatics Cluster, University of Central Florida, Orlando, FL, USA
| |
Collapse
|
213
|
Keller AG, Grason EW, McDonald PS, Ramón-Laca A, Kelly RP. Tracking an invasion front with environmental DNA. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2561. [PMID: 35128750 DOI: 10.1002/eap.2561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 12/14/2021] [Indexed: 05/03/2023]
Abstract
Data from environmental DNA (eDNA) may revolutionize environmental monitoring and management, providing increased detection sensitivity at reduced cost and survey effort. However, eDNA data are rarely used in decision-making contexts, mainly due to uncertainty around (1) data interpretation and (2) whether and how molecular tools dovetail with existing management efforts. We address these challenges by jointly modeling eDNA detection via qPCR and traditional trap data to estimate the density of invasive European green crab (Carcinus maenas), a species for which, historically, baited traps have been used for both detection and control. Our analytical framework simultaneously quantifies uncertainty in both detection methods and provides a robust way of integrating different data streams into management processes. Moreover, the joint model makes clear the marginal information benefit of adding eDNA (or any other) additional data type to an existing monitoring program, offering a path to optimizing sampling efforts for species of management interest. Here, we document green crab eDNA beyond the previously known invasion front and find that the value of eDNA data dramatically increases with low population densities and low traditional sampling effort, as is often the case at leading-edge locations. We also highlight the detection limits of the molecular assay used in this study, as well as scenarios under which eDNA sampling is unlikely to improve existing management efforts.
Collapse
Affiliation(s)
- Abigail G Keller
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | - Emily W Grason
- Washington Sea Grant, University of Washington, Seattle, Washington, USA
| | - P Sean McDonald
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Ana Ramón-Laca
- CICOES, University of Washington at Northwest Fisheries Science Center, Seattle, Washington, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| |
Collapse
|
214
|
Czech L, Stamatakis A, Dunthorn M, Barbera P. Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade. FRONTIERS IN BIOINFORMATICS 2022; 2:871393. [PMID: 36304302 PMCID: PMC9580882 DOI: 10.3389/fbinf.2022.871393] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based) methods, it puts metabarcoding sequences into a phylogenetic context using a set of known reference sequences and taking evolutionary history into account. Thereby, one can increase the accuracy of metagenomic surveys and eliminate the requirement for having exact or close matches with existing sequence databases. Phylogenetic placement constitutes a valuable analysis tool per se, but also entails a plethora of downstream tools to interpret its results. A common use case is to analyze species communities obtained from metagenomic sequencing, for example via taxonomic assignment, diversity quantification, sample comparison, and identification of correlations with environmental variables. In this review, we provide an overview over the methods developed during the first 10 years. In particular, the goals of this review are 1) to motivate the usage of phylogenetic placement and illustrate some of its use cases, 2) to outline the full workflow, from raw sequences to publishable figures, including best practices, 3) to introduce the most common tools and methods and their capabilities, 4) to point out common placement pitfalls and misconceptions, 5) to showcase typical placement-based analyses, and how they can help to analyze, visualize, and interpret phylogenetic placement data.
Collapse
Affiliation(s)
- Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway
| | | |
Collapse
|
215
|
Miya M, Sado T, Oka SI, Fukuchi T. The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.80444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To test the feasibility of a citizen science program for fish eDNA metabarcoding in coastal marine environments, we recruited six groups of voluntary citizens for a science education course at a natural history museum. We held a seminar on eDNA and a workshop for seawater sampling and on-site filtration using syringes and filter cartridges for the participants. After that, they selected single survey sites following the guidelines for conducting a safe field trip. They performed seawater sampling and on-site filtration at these sites during their summer holidays. The six selected sites unexpectedly included diverse coastal habitats within a 40 km radius, located at temperate latitudes in central Japan (~35°N). After the field trips, they returned filtered cartridges to the museum, and we extracted eDNA from the filters. We performed fish eDNA metabarcoding, along with data analysis. Consequently, we identified 140 fish species across 66 families and 118 genera from the six samples, with species richness ranging from 14 to 66. Despite its limited sample size, such a diverse taxonomic range of fish species exhibited spatial biodiversity patterns within the region, which are consistent with species distribution. These include north-south and urbanization gradients of species richness, geographic structure of the fish communities, and varying salinity preferences of the component species. This case study demonstrates the potential of fish eDNA metabarcoding as an educational and scientific tool to raise public awareness and perform large-scale citizen science initiatives encompassing regional, national, or global fauna.
Collapse
|
216
|
Galanis A, Vardakas P, Reczko M, Harokopos V, Hatzis P, Skoulakis EMC, Pavlopoulos GA, Patalano S. Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey. Mol Ecol Resour 2022; 22:2506-2523. [PMID: 35593171 DOI: 10.1111/1755-0998.13626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 02/14/2022] [Accepted: 04/13/2022] [Indexed: 11/26/2022]
Abstract
Honeybees (Apis mellifera) continue to succumb to human and environmental pressures despite their crucial role in providing essential ecosystem services. Owing to their foraging and honey production activities, honeybees form complex relationships with species across all domains, such as plants, viruses, bacteria and other hive pests, making honey a valuable biomonitoring tool for assessing their ecological niche. Thus, the application of honey shotgun metagenomics (SM) has paved the way for a detailed description of the species honeybees interact with. Nevertheless, SM bioinformatics tools and DNA extraction methods rely on resources not necessarily optimized for honey. In this study, we compared five widely used taxonomic classifiers using simulated species communities commonly found in honey. We found that Kraken 2 with a threshold of 0.5 performs best in assessing species distribution. We also optimized a simple NaOH-based honey DNA extraction methodology (Direct-SM), which profiled species seasonal variability similarly to an established column-based DNA extraction approach (SM). Both approaches produce results consistent with melissopalinology analysis describing the botanical landscape surrounding the apiary. Interestingly, we detected a strong stability of the bacteria constituting the core and noncore gut microbiome across seasons, pointing to the potential utility of honey for noninvasive assessment of bee microbiota. Finally, the Direct-SM approach to detect Varroa correlates well with the biomonitoring of mite infestation observed in hives. These observations suggest that Direct-SM methodology has the potential to comprehensively describe honeybee ecological niches and can be tested as a building block for large-scale studies to assess bee health in the field.
Collapse
Affiliation(s)
- Anastasios Galanis
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece.,Division of Animal and Human Physiology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Philippos Vardakas
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece.,Department of Apiculture, Institute of Animal Science, Nea Moudania, Greece
| | - Martin Reczko
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| | - Vaggelis Harokopos
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| | - Efthimios M C Skoulakis
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| | - Georgios A Pavlopoulos
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| | - Solenn Patalano
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| |
Collapse
|
217
|
Diversity, distribution and ecology of fungal communities present in Antarctic lake sediments uncovered by DNA metabarcoding. Sci Rep 2022; 12:8407. [PMID: 35589789 PMCID: PMC9120451 DOI: 10.1038/s41598-022-12290-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/29/2022] [Indexed: 01/04/2023] Open
Abstract
We assessed fungal diversity in sediments obtained from four lakes in the South Shetland Islands and James Ross Island, Antarctica, using DNA metabarcoding. We detected 218 amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota and Chytridiomycota. In addition, the rare phyla Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Monoblepharomycota, Rozellomycota and Zoopagomycota as well as fungal-like Straminopila belonging to the phyla Bacillariophyta and Oomycota were detected. The fungal assemblages were dominated by unknown fungal taxa (Fungal sp. 1 and Fungal sp. 2), followed by Talaromyces rubicundus and Dactylonectria anthuriicola. In general, they displayed high diversity, richness and moderate dominance. Sequences representing saprophytic, pathogenic and symbiotic fungi were detected, including the phytopathogenic fungus D. anthuriicola that was abundant, in the relatively young Soto Lake on Deception Island. The lake sediments studied contained the DNA of rich, diverse and complex fungal communities, including both fungi commonly reported in Antarctica and other taxa considered to be rare. However, as the study was based on the use of environmental DNA, which does not unequivocally confirm the presence of active or viable organisms, further studies using other approaches such as shotgun sequencing are required to elucidate the ecology of fungi in these Antarctic lake sediments.
Collapse
|
218
|
Bessey C, Gao Y, Truong YB, Miller H, Jarman SN, Berry O. Comparison of materials for rapid passive collection of environmental
DNA. Mol Ecol Resour 2022; 22:2559-2572. [PMID: 35570323 PMCID: PMC9544503 DOI: 10.1111/1755-0998.13640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/24/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive and efficient, and requires minimal equipment, making it suited to high‐density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3‐million‐litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibres and 1% chitosan, cotton fibres, hemp fibres, and sponge with either zeolite or active carbon) for intervals between 5 and 1080 min. We show that for most materials, with as little as 5 min of submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 and 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19–32). Using scanning electron microscopy, we visualized biological matter adhering to the surface of materials, rather than entrapped, with images also revealing a diversity in size and structure of putative eDNA particles. eDNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost‐ and time‐sensitive biological surveys, and where access to equipment is limited.
Collapse
Affiliation(s)
- Cindy Bessey
- Commonwealth Scientific and Industrial Research Organisation, Indian Oceans Marine Research Centre, Oceans and Atmosphere, 64 Fairway Crawley WA Australia
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
- University of Western Australia UWA Oceans Institute, 35 Stirling Highway Crawley WA Australia
| | - Yuan Gao
- Commonwealth Scientific and Industrial Research Organization, Manufacturing, Research Way Clayton Australia
| | - Yen Bach Truong
- Commonwealth Scientific and Industrial Research Organization, Manufacturing, Research Way Clayton Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
| | - Simon Neil Jarman
- University of Western Australia UWA Oceans Institute, 35 Stirling Highway Crawley WA Australia
- University of Western Australia School of Biological Sciences and the UWA Oceans Institute Crawley WA Australia
| | - Oliver Berry
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, 64 Fairway Crawley WA Australia
| |
Collapse
|
219
|
Shinohara N, Hongo Y, Ichinokawa M, Nishijima S, Sawayama S, Kurogi H, Uto Y, Mita H, Ishii M, Kusano A, Akimoto S. Similar fish species composition despite larger environmental heterogeneity during severe hypoxia in a coastal ecosystem. Ecol Evol 2022; 12:e8884. [PMID: 35600699 PMCID: PMC9108318 DOI: 10.1002/ece3.8884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022] Open
Abstract
Environmental heterogeneity is one of the most influential factors that create compositional variation among local communities. Greater compositional variation is expected when an environmental gradient encompasses the most severe conditions where species sorting is more likely to operate. However, evidence for stronger species sorting at severer environment has typically been obtained for less mobile organisms and tests are scarce for those with higher dispersal ability that allows individuals to sensitively respond to environmental stress. Here, with the dynamics of fish communities in a Japanese bay revealed by environmental DNA metabarcoding analyses as a model case, we tested the hypothesis that larger environmental heterogeneity caused by severe seasonal hypoxia (lower concentration of oxygen in bottom waters in summer) leads to larger variation of species composition among communities. During summer, fish species richness was lower in the bottom layer, suggesting the severity of the hypoxic bottom water. In contrast to the prediction, we found that although the environmental parameters of bottom and surface water was clearly distinct in summer, fish species composition was more similar between the two layers. Our null model analysis suggested that the higher compositional similarity during hypoxia season was not a result of the sampling effect reflecting differences in the alpha or gamma diversity. Furthermore, a shift in the species occurrence from bottom to surface layers was observed during hypoxia season, which was consistent across species, suggesting that the severe condition in the bottom adversely affected fish species irrespective of their identity. These results suggest that larger environmental heterogeneity does not necessarily lead to higher compositional variation once the environmental gradient encompasses extremely severe conditions. This is most likely because individual organisms actively avoided the severity quasi‐neutrally, which induced mass effect‐like dispersal and lead to the mixing of species composition across habitats. By showing counter evidence against the prevailing view, we provide novel insights into how species sorting by environment acts in heterogeneous and severe conditions.
Collapse
Affiliation(s)
- Naoto Shinohara
- Fisheries Resources Institute Japan Fisheries Research and Education Agency Yokohama Japan
| | - Yuki Hongo
- Fisheries Resources Institute Japan Fisheries Research and Education Agency Yokohama Japan
| | - Momoko Ichinokawa
- Fisheries Resources Institute Japan Fisheries Research and Education Agency Yokohama Japan
| | - Shota Nishijima
- Fisheries Resources Institute Japan Fisheries Research and Education Agency Yokohama Japan
| | - Shuhei Sawayama
- Fisheries Resources Institute Japan Fisheries Research and Education Agency Yokohama Japan
| | - Hiroaki Kurogi
- Fisheries Resources Institute Japan Fisheries Research and Education Agency Yokohama Japan
| | - Yasuyuki Uto
- Marine Industries Promotion Division Chiba Prefectural Government Chiba Japan
| | - Hisanori Mita
- Chiba Prefectural Fisheries Research Center Chiba Japan
| | | | - Akane Kusano
- Fisheries Division Environment and Agriculture Bureau Kanagawa Prefectural Government Yokohama Japan
| | - Seiji Akimoto
- Fisheries Research Institute of Kanagawa Prefecture Yokohama Japan
| |
Collapse
|
220
|
Molik DC. met v1: expanding on old estimations of biodiversity from eDNA with a new database framework. Database (Oxford) 2022; 2022:6583522. [PMID: 35543254 PMCID: PMC9216496 DOI: 10.1093/database/baac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/10/2022] [Accepted: 04/28/2022] [Indexed: 11/14/2022]
Abstract
Abstract
A long-standing problem in environmental DNA has been the inability to compute across large number of datasets. Here we introduce an open-source software framework that can store a large number of environmental DNA datasets, as well as provide a platform for analysis, in an easily customizable way. We show the utility of such an approach by analyzing over 1400 arthropod metabarcode datasets. This article introduces a new software framework, met, which utilizes large numbers of metabarcode datasets to draw conclusions about patterns of diversity at large spatial scales. Given more accurate estimations on the distribution of variance in metabarcode datasets, this software framework could facilitate novel analyses that are outside the scope of currently available similar platforms.
Database URL https://osf.io/spb8v/
Collapse
Affiliation(s)
- David C Molik
- Navari Family Center for Digital Scholarship, Hesburgh Library, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA
| |
Collapse
|
221
|
Saccò M, Guzik MT, van der Heyde M, Nevill P, Cooper SJB, Austin AD, Coates PJ, Allentoft ME, White NE. eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153223. [PMID: 35063529 DOI: 10.1016/j.scitotenv.2022.153223] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.
Collapse
Affiliation(s)
- Mattia Saccò
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia.
| | - Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Mieke van der Heyde
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide 5000, SA, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Peterson J Coates
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, 1006, Dartmouth, Nova Scotia B2Y 4A2, Canada
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Nicole E White
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| |
Collapse
|
222
|
Jones L, Lowe A, Ford CR, Christie L, Creer S, de Vere N. Temporal Patterns of Honeybee Foraging in a Diverse Floral Landscape Revealed Using Pollen DNA Metabarcoding of Honey. Integr Comp Biol 2022; 62:199-210. [PMID: 35536572 PMCID: PMC9405717 DOI: 10.1093/icb/icac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/21/2022] [Accepted: 05/08/2022] [Indexed: 11/15/2022] Open
Abstract
Understanding the plants pollinators use through the year is vital to support pollinator populations and mitigate for declines in floral resources due to habitat loss. DNA metabarcoding allows the temporal picture of nectar and pollen foraging to be examined in detail. Here, we use DNA metabarcoding to examine the forage use of honeybees (Apis mellifera L.) within a florally diverse landscape within the UK, documenting the key forage plants used and seasonal progression over two years. The total number of plant taxa detected in the honey was 120, but only 16 of these were found with a high relative read abundance of DNA, across the main foraging months (April-September). Only a small proportion of the available flowering genera in the landscape were used by the honeybees. The greatest relative read abundance came from native or near-native plants, including Rubus spp., Trifolium repens, the Maleae tribe including Crataegus, Malus and Cotoneaster, and Hedera helix. Tree species were important forage in the spring months, followed by increased use of herbs and shrubs later in the foraging season. Garden habitat increased the taxon richness of native, near-native and horticultural plants found in the honey. Although horticultural plants were rarely found abundantly within the honey samples, they may be important for increasing nutritional diversity of the pollen forage.
Collapse
Affiliation(s)
- Laura Jones
- National Botanic Garden of Wales, Llanarthne, UK
| | - Abigail Lowe
- National Botanic Garden of Wales, Llanarthne, UK
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Col R Ford
- Spirent Communications, Positioning Technology, Crawley, West Sussex, UK
| | | | - Simon Creer
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | | |
Collapse
|
223
|
Keck F, Hürlemann S, Locher N, Stamm C, Deiner K, Altermatt F. A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.79351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
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.
Collapse
|
224
|
Gregorič M, Kutnjak D, Bačnik K, Gostinčar C, Pecman A, Ravnikar M, Kuntner M. Spider webs as eDNA samplers: biodiversity assessment across the tree of life. Mol Ecol Resour 2022; 22:2534-2545. [PMID: 35510791 DOI: 10.1111/1755-0998.13629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/03/2022] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Abstract
The concept of environmental DNA (eDNA) utilizes nucleic acids of organisms directly from the environment. Recent breakthrough studies have successfully detected a wide spectrum of prokaryotic and eukaryotic eDNA from a variety of environments, ranging from ancient to modern, and from terrestrial to aquatic. With their diversity and ubiquity in nature, spider webs might act as powerful biofilters and could thus represent a promising new source of eDNA, but their utility under natural field conditions is severely understudied. Here, we bridge this knowledge gap to establish spider webs as a source of eDNA with far reaching implications. First, we conducted a field study to track specific arthropod targets from different spider webs. We then employed high-throughput amplicon sequencing of taxonomic barcodes to investigate the utility of spider web eDNA for biodiversity monitoring of animals, fungi, and bacteria. Our results show that genetic remains on spider webs allow the detection of even the smallest target organisms. We also demonstrate that eDNA from spider webs is useful in research of community compositions across the different domains of life, with potentially highly detailed temporal and spatial information.
Collapse
Affiliation(s)
- Matjaž Gregorič
- Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, 1000, Ljubljana, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Katarina Bačnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ulica 101, 1000, Ljubljana, Slovenia
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Wine Research Centre, University of Nova Gorica, Vipavska 13, 5000, Nova Gorica, Slovenia
| | - Matjaž Kuntner
- Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, 1000, Ljubljana, Slovenia.,Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, NW, Washington DC, 20560-0105, USA.,Centre for Behavioural Ecology and Evolution, College of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei, 430062, China
| |
Collapse
|
225
|
Mauvisseau Q, Harper LR, Sander M, Hanner RH, Kleyer H, Deiner K. The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5322-5333. [PMID: 35435663 PMCID: PMC9069692 DOI: 10.1021/acs.est.1c07638] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Increased use of environmental DNA (eDNA) analysis for indirect species detection has spurred the need to understand eDNA persistence in the environment. Understanding the persistence of eDNA is complex because it exists in a mixture of different states (e.g., dissolved, particle adsorbed, intracellular, and intraorganellar), and each state is expected to have a specific decay rate that depends on environmental parameters. Thus, improving knowledge about eDNA conversion rates between states and the reactions that degrade eDNA in different states is needed. Here, we focus on eukaryotic extraorganismal eDNA, outline how water chemistry and suspended mineral particles likely affect conversion among each eDNA state, and indicate how environmental parameters affect persistence of states in the water column. On the basis of deducing these controlling parameters, we synthesized the eDNA literature to assess whether we could already derive a general understanding of eDNA states persisting in the environment. However, we found that these parameters are often not being measured or reported when measured, and in many cases very few experimental data exist from which to draw conclusions. Therefore, further study of how environmental parameters affect eDNA state conversion and eDNA decay in aquatic environments is needed. We recommend analytic controls that can be used during the processing of water to assess potential losses of different eDNA states if all were present in a water sample, and we outline future experimental work that would help determine the dominant eDNA states in water.
Collapse
Affiliation(s)
- Quentin Mauvisseau
- Natural
History Museum, University of Oslo, Sars’ gate 1, 0562 Oslo, Norway
| | - Lynsey R. Harper
- Nature
Metrics Ltd, CABI Site, Bakeham Lane, Egham, Surrey TW20 9TY, United Kingdom
| | - Michael Sander
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
| | - Robert H. Hanner
- Department
of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hannah Kleyer
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
| | - Kristy Deiner
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
| |
Collapse
|
226
|
Rosa LH, Ogaki MB, Lirio JM, Vieira R, Coria SH, Pinto OHB, Carvalho-Silva M, Convey P, Rosa CA, Câmara PEAS. Fungal diversity in a sediment core from climate change impacted Boeckella Lake, Hope Bay, north-eastern Antarctic Peninsula assessed using metabarcoding. Extremophiles 2022; 26:16. [PMID: 35499659 DOI: 10.1007/s00792-022-01264-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/05/2022] [Indexed: 01/04/2023]
Abstract
We studied the fungal DNA present in a lake sediment core obtained from Trinity Peninsula, Hope Bay, north-eastern Antarctic Peninsula, using metabarcoding through high-throughput sequencing (HTS). Sequences obtained were assigned to 146 amplicon sequence variants (ASVs) primarily representing unknown fungi, followed by the phyla Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota and Mortierellomycota. The most abundant taxa were assigned to Fungal sp., Pseudeurotium hygrophilum, Rozellomycota sp. 1, Pseudeurotiaceae sp. 1 and Chytridiomycota sp. 1. The majority of the DNA reads, representing 40 ASVs, could only be assigned at higher taxonomic levels and may represent taxa not currently included in the sequence databases consulted and/or be previously undescribed fungi. Different sections of the core were characterized by high sequence diversity, richness and moderate ecological dominance indices. The assigned diversity was dominated by cosmopolitan cold-adapted fungi, including known saprotrophic, plant and animal pathogenic and symbiotic taxa. Despite the overall dominance of Ascomycota and Basidiomycota and psychrophilic Mortierellomycota, members of the cryptic phyla Rozellomycota and Chytridiomycota were also detected in abundance. As Boeckella Lake may cease to exist in approaching decades due the effects of local climatic changes, it also an important location for the study of the impacts of these changes on Antarctic microbial diversity.
Collapse
Affiliation(s)
- Luiz Henrique Rosa
- Laboratório de Microbiologia Polar e Conexões Tropicais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, PO Box 486, Belo Horizonte, MG, 31270-901, Brazil.
| | - Mayara Baptistucci Ogaki
- Laboratório de Microbiologia Polar e Conexões Tropicais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, PO Box 486, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Rosemary Vieira
- Instituto de Geociências, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | | | | | | | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.,Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park, 2006, South Africa
| | - Carlos Augusto Rosa
- Laboratório de Microbiologia Polar e Conexões Tropicais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, PO Box 486, Belo Horizonte, MG, 31270-901, Brazil
| | | |
Collapse
|
227
|
Maslakova S, Ellison CI, Hiebert TC, Conable F, Heaphy MC, Venera-Pontón DE, Norenburg JL, Schwartz ML, Moss ND, Boyle MJ, Driskell AC, Macdonald KS, Zattara EE, Collin R. Sampling multiple life stages significantly increases estimates of marine biodiversity. Biol Lett 2022; 18:20210596. [PMID: 35414224 PMCID: PMC9039783 DOI: 10.1098/rsbl.2021.0596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Biodiversity assessments are critical for setting conservation priorities, understanding ecosystem function and establishing a baseline to monitor change. Surveys of marine biodiversity that rely almost entirely on sampling adult organisms underestimate diversity because they tend to be limited to habitat types and individuals that can be easily surveyed. Many marine animals have planktonic larvae that can be sampled from the water column at shallow depths. This life stage often is overlooked in surveys but can be used to relatively rapidly document diversity, especially for the many species that are rare or live cryptically as adults. Using DNA barcode data from samples of nemertean worms collected in three biogeographical regions—Northeastern Pacific, the Caribbean Sea and Eastern Tropical Pacific—we found that most species were collected as either benthic adults or planktonic larvae but seldom in both stages. Randomization tests show that this deficit of operational taxonomic units collected as both adults and larvae is extremely unlikely if larvae and adults were drawn from the same pool of species. This effect persists even in well-studied faunas. These results suggest that sampling planktonic larvae offers access to a different subset of species and thus significantly increases estimates of biodiversity compared to sampling adults alone. Spanish abstract is available in the electronic supplementary material.
Collapse
Affiliation(s)
- Svetlana Maslakova
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Christina I Ellison
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Terra C Hiebert
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Frances Conable
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Maureen C Heaphy
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | | | - Jon L Norenburg
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Megan L Schwartz
- University of Washington, 1900 Commerce Avenue, Tacoma, WA 98420, USA
| | - Nicole D Moss
- Oregon Institute of Marine Biology, 63466 Boat Basin Road, Charleston, OR 97420, USA
| | - Michael J Boyle
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama
| | - Amy C Driskell
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Eduardo E Zattara
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,INIBIOMA, Universidad Nacional del Comahue-CONICET, Bariloche, Río Negro, 8400, Argentina
| | - Rachel Collin
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama
| |
Collapse
|
228
|
Ariza M, Fouks B, Mauvisseau Q, Halvorsen R, Alsos IG, de Boer H. Plant biodiversity assessment through soil
eDNA
reflects temporal and local diversity. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- María Ariza
- Universitetet i Oslo, Naturhistorisk Museum Oslo Norway
| | - Bertrand Fouks
- Westfälische Wilhelms‐Universität Institute for Evolution and Biodiversity Molecular Evolution and Bioinformatics. Hüfferstraße 1 Münster Germany
| | | | | | - Inger Greve Alsos
- The Arctic University Museum of Norway UiT ‐ The Arctic University of Norway Norway
| | - Hugo de Boer
- Universitetet i Oslo, Naturhistorisk Museum Oslo Norway
| |
Collapse
|
229
|
Foster NR, Dijk K, Biffin E, Young JM, Thomson VA, Gillanders BM, Jones AR, Waycott M. A targeted capture approach to generating reference sequence databases for chloroplast gene regions. Ecol Evol 2022; 12:e8816. [PMID: 35432922 PMCID: PMC9001157 DOI: 10.1002/ece3.8816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Nicole R. Foster
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Kor‐jent Dijk
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Ed Biffin
- State Herbarium of South Australia Botanic Gardens and State Herbarium Adelaide South Australia Australia
| | - Jennifer M. Young
- College of Science and Engineering Flinders University South Australia Australia
| | - Vicki A. Thomson
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Bronwyn M. Gillanders
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Alice R. Jones
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Michelle Waycott
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
- State Herbarium of South Australia Botanic Gardens and State Herbarium Adelaide South Australia Australia
| |
Collapse
|
230
|
Heil JA, Wolock CJ, Pierce NE, Pringle A, Bittleston LS. Sarracenia pitcher plant-associated microbial communities differ primarily by host species across a longitudinal gradient. Environ Microbiol 2022; 24:3500-3516. [PMID: 35384233 DOI: 10.1111/1462-2920.15993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/18/2022] [Accepted: 03/31/2022] [Indexed: 11/27/2022]
Abstract
Plant-associated microbial communities can profoundly affect plant health and success, and research is still uncovering factors driving the assembly of these communities. Here, we examine how geography versus host species affect microbial community structure and differential abundances of individual taxa. We use metabarcoding to characterize the bacteria and eukaryotes associated with five, often co-occurring species of Sarracenia pitcher plants (Sarraceniaceae) and three natural hybrids along the longitudinal gradient of the U.S. Gulf Coast, as well as samples from S. purpurea in Massachusetts. To tease apart the effects of geography versus host species, we focus first on sites with co-occurring species and then on species located across different sites. Our analyses show that bacterial and eukaryotic community structures are clearly and consistently influenced by host species identity, with geographic factors also playing a role. Naturally-occurring hybrids appear to also host unique communities, that are in some ways intermediate between their parent species. We see significant effects of geography (site and longitude), but these generally explain less of the variation among pitcher communities. Overall, in Sarracenia pitchers, host plant phenotype significantly affects the pitcher microbiomes and other associated organisms. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Jacob A Heil
- Department of Biological Sciences, Boise State University
| | | | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin-Madison
| | | |
Collapse
|
231
|
Saeed M, Rais M, Akram A, Williams MR, Kellner KF, Hashsham SA, Davis DR. Development and validation of an eDNA protocol for monitoring endemic Asian spiny frogs in the Himalayan region of Pakistan. Sci Rep 2022; 12:5624. [PMID: 35379841 PMCID: PMC8979970 DOI: 10.1038/s41598-022-09084-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both A. hazarensis and N. vicina than for visual encounter surveys. Detection probability using eDNA was greater for both species, particularly for A. hazarensis. The top-ranked detection model for visual encounter surveys included effects of both year and temperature on both species, and the top-ranked occupancy model included effects of elevation and year. The top-ranked detection model for eDNA data was the null model, and the top-ranked occupancy model included effects of elevation, year, and wetland type. To our knowledge, this is the first time an eDNA survey has been used to monitor amphibian species in the Himalayan region.
Collapse
Affiliation(s)
- Muhammad Saeed
- Herpetology Lab, Department of Wildlife Management, Faculty of Forestry, Range Management and Wildlife, Pir Mehr Ali Shah, Arid Agriculture University Rawalpindi, Rawalpindi, 46000, Pakistan. .,Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
| | - Muhammad Rais
- Herpetology Lab, Department of Wildlife Management, Faculty of Forestry, Range Management and Wildlife, Pir Mehr Ali Shah, Arid Agriculture University Rawalpindi, Rawalpindi, 46000, Pakistan.
| | - Ayesha Akram
- Herpetology Lab, Department of Wildlife Management, Faculty of Forestry, Range Management and Wildlife, Pir Mehr Ali Shah, Arid Agriculture University Rawalpindi, Rawalpindi, 46000, Pakistan
| | - Maggie R Williams
- School of Engineering and Technology, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA
| | - Kenneth F Kellner
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.,Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.,Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Drew R Davis
- School of Earth, Environmental, and Marine Science, The University of Texas Rio Grande Valley, Brownsville, TX, USA.,Biodiversity Collections, Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
232
|
Mailli AA, Jakt LM, Reiss H, Kopp ME, Moum TB. Exploring the potential of mRNA for taxonomic delineation of marine benthic eukaryotes. Mar Genomics 2022; 62:100934. [DOI: 10.1016/j.margen.2022.100934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
|
233
|
Ionescu D, Bizic M, Karnatak R, Musseau CL, Onandia G, Kasada M, Berger SA, Nejstgaard JC, Ryo M, Lischeid G, Gessner MO, Wollrab S, Grossart H. From microbes to mammals: Pond biodiversity homogenization across different land‐use types in an agricultural landscape. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- D. Ionescu
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Bizic
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - R. Karnatak
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - C. L. Musseau
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology Free University of Berlin Germany
| | - G. Onandia
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. Kasada
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
| | - S. A. Berger
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - J. C. Nejstgaard
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Ryo
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
- Brandenburg University of Technology Cottbus–Senftenberg Cottbus Germany
| | - G. Lischeid
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. O. Gessner
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Ecology Berlin Institute of Technology (TU Berlin) Berlin Germany
| | - S. Wollrab
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - H.‐P. Grossart
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Institute of Biochemistry and Biology Potsdam University Potsdam Germany
| |
Collapse
|
234
|
de Menezes GCA, Câmara PEAS, Pinto OHB, Convey P, Carvalho-Silva M, Simões JC, Rosa CA, Rosa LH. Fungi in the Antarctic Cryosphere: Using DNA Metabarcoding to Reveal Fungal Diversity in Glacial Ice from the Antarctic Peninsula Region. MICROBIAL ECOLOGY 2022; 83:647-657. [PMID: 34228196 DOI: 10.1007/s00248-021-01792-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
We assessed fungal diversity present in glacial from the Antarctic Peninsula using DNA metabarcoding through high-throughput sequencing (HTS). We detected a total of 353,879 fungal DNA reads, representing 94 genera and 184 taxa, in glacial ice fragments obtained from seven sites in the north-west Antarctic Peninsula and South Shetland Islands. The phylum Ascomycota dominated the sequence diversity, followed by Basidiomycota and Mortierellomycota. Penicillium sp., Cladosporium sp., Penicillium atrovenetum, Epicoccum nigrum, Pseudogymnoascus sp. 1, Pseudogymnoascus sp. 2, Phaeosphaeriaceae sp. and Xylaria grammica were the most dominant taxa, respectively. However, the majority of the fungal diversity comprised taxa of rare and intermediate relative abundance, predominately known mesophilic fungi. High indices of diversity and richness were calculated, along with moderate index of dominance, which varied among the different sampling sites. Only 26 (14%) of the total fungal taxa detected were present at all sampling sites. The identified diversity was dominated by saprophytic taxa, followed by known plant and animal pathogens and a low number of symbiotic fungi. Our data suggest that Antarctic glacial ice may represent a hotspot of previously unreported fungal diversity; however, further studies are required to integrate HTS and culture approaches to confirm viability of the taxa detected.
Collapse
Affiliation(s)
- Graciéle Cunha Alves de Menezes
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, , CEP 31270-901, Brazil
| | | | | | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Zoology , University of Johannesburg , Johannesburg, South Africa
| | | | - Jefferson Cardia Simões
- Centro Polar E Climático, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carlos Augusto Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, , CEP 31270-901, Brazil
| | - Luiz Henrique Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, , CEP 31270-901, Brazil.
| |
Collapse
|
235
|
Papaiakovou M, Littlewood DTJ, Doyle SR, Gasser RB, Cantacessi C. Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics-metabolomics. Parasit Vectors 2022; 15:118. [PMID: 35365192 PMCID: PMC8973539 DOI: 10.1186/s13071-022-05225-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023] Open
Abstract
Gastrointestinal (GI) helminth infections cause significant morbidity in both humans and animals worldwide. Specific and sensitive diagnosis is central to the surveillance of such infections and to determine the effectiveness of treatment strategies used to control them. In this article, we: (i) assess the strengths and limitations of existing methods applied to the diagnosis of GI helminth infections of humans and livestock; (ii) examine high-throughput sequencing approaches, such as targeted molecular barcoding and shotgun sequencing, as tools to define the taxonomic composition of helminth infections; and (iii) discuss the current understanding of the interactions between helminths and microbiota in the host gut. Stool-based diagnostics are likely to serve as an important tool well into the future; improved diagnostics of helminths and their environment in the gut may assist the identification of biomarkers with the potential to define the health/disease status of individuals and populations, and to identify existing or emerging anthelmintic resistance.
Collapse
Affiliation(s)
- Marina Papaiakovou
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | | | | | - Robin B. Gasser
- Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
| |
Collapse
|
236
|
Ghanam J, Chetty VK, Barthel L, Reinhardt D, Hoyer PF, Thakur BK. DNA in extracellular vesicles: from evolution to its current application in health and disease. Cell Biosci 2022; 12:37. [PMID: 35346363 PMCID: PMC8961894 DOI: 10.1186/s13578-022-00771-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/07/2022] [Indexed: 02/08/2023] Open
Abstract
Extracellular vesicle (EV) secretion is a highly conserved evolutionary trait in all organisms in the three domains of life. The packaging and release of EVs appears to be a bulk-flow process which takes place mainly under extreme conditions. EVs participate in horizontal gene transfer, which supports the survival of prokaryotic and eukaryotic microbes. In higher eukaryotes, almost all cells secrete a heterogeneous population of EVs loaded with various biomolecules. EV secretion is typically higher in cancer microenvironments, promoting tumor progression and metastasis. EVs are now recognized as additional mediators of autocrine and paracrine communication in health and disease. In this context, proteins and RNAs have been studied the most, but extracellular vesicle DNA (EV-DNA) has started to gain in importance in the last few years. In this review, we summarize new findings related to the loading mechanism(s), localization, and post-shedding function of EV-DNA. We also discuss the feasibility of using EV-DNA as a biomarker when performing a liquid biopsy, at the same time emphasizing the lack of data from clinical trials in this regard. Finally, we outline the potential of EV-DNA uptake and its interaction with the host genome as a promising tool for understanding the mechanisms of cancer evolution. Protecting DNA in membrane vesicles seems to be a conserved phenomenon for the horizontal genetic flux between prokaryotes and lower eukaryotes. Capturing and analyzing this vesicular DNA enables quick and non-invasive monitoring of natural ecosystems. Cancer-derived extracellular vesicles containing DNA open up novel directions in cell-to-cell communication and therefore disease monitoring. Complex and fluctuating conditions of the tumor microenvironment, mimicking natural ecosystems, could favor EV-DNA release, mediating tumor multi-clonal evolution and providing survival benefits.
Collapse
Affiliation(s)
- Jamal Ghanam
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Venkatesh Kumar Chetty
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Lennart Barthel
- Department of Neurosurgery and Spine Surgery, Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, 45147, Essen, Germany.,Institute of Medical Psychology and Behavioral Immunobiology, Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, 45147, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Peter-Friedrich Hoyer
- Department of Pediatrics II, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Basant Kumar Thakur
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany.
| |
Collapse
|
237
|
Abstract
The identification of floral visitation by pollinators provides an opportunity to improve our understanding of the fine-scale ecological interactions between plants and pollinators, contributing to biodiversity conservation and promoting ecosystem health. In this review, we outline the various methods which can be used to identify floral visitation, including plant-focused and insect-focused methods. We reviewed the literature covering the ways in which DNA metabarcoding has been used to answer ecological questions relating to plant use by pollinators and discuss the findings of this research. We present detailed methodological considerations for each step of the metabarcoding workflow, from sampling through to amplification, and finally bioinformatic analysis. Detailed guidance is provided to researchers for utilisation of these techniques, emphasising the importance of standardisation of methods and improving the reliability of results. Future opportunities and directions of using molecular methods to analyse plant–pollinator interactions are then discussed.
Collapse
|
238
|
Highly sensitive environmental DNA detection of topmouth gudgeon, Pseudorasbora parva: a comparison of qPCR and microfluidic qdPCR. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AbstractTopmouth gudgeon is a freshwater fish species native to East Asia. Nowadays, P. parva is spread throughout Europe which is of concern because besides being considered one of the worst aquatic Invasive Alien Species (IAS) in Europe it is also a known vector of Spherotecum destruens, the rosette-like parasite lethal to other fish species. The present study describes the development and validation of a new species-specific assay based on hydrolysis probe chemistry to detect P. parva environmental DNA (eDNA) in water samples collected in a northern region of Italy (Friuli Venezia Giulia). Water samples were collected from 55 sites in an area where partial information on the occurrence of the species is available. eDNA was isolated from all samples and the presence of P. parva eDNA was tested by means of qPCR (quantitative PCR) and microfluidic qdPCR (quantitative digital PCR) techniques. Field results for both qPCR and qdPCR were largely in agreement in terms of detection (presence/absence). Thus, we judged the presence/absence by combining the results from the two methods and found that nine sites showed “strong positive” signal of P. parva eDNA (at least 2 positive replicates), 3 showed “suspected” (only 1 positive replicate), and 42 showed “absent”. The current study shows the strong potential of the newly developed eDNA approach to be a valuable addition to the monitoring of the highly invasive topmouth gudgeon in freshwater ecosystems.
Collapse
|
239
|
Holman LE, Parker-Nance S, de Bruyn M, Creer S, Carvalho G, Rius M. Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210025. [PMID: 35067092 PMCID: PMC8784926 DOI: 10.1098/rstb.2021.0025] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The use of molecular tools to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species' range shifts. This is important when managing range shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here, we investigated the ascidian NNS Ciona robusta, Clavelina lepadiformis, Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NNS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the biodiversity survey and the COI datasets, but failed to capture the complete incidence of all NNS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing both thriving NNS and threatened species. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.
Collapse
Affiliation(s)
- Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - Shirley Parker-Nance
- Zoology Department, Institute for Coastal and Marine Research Nelson Mandela University Ocean Sciences Campus, Gqeberha (Port Elizabeth), South Africa.,South African Environmental Observation Network (SAEON) Elwandle Coastal Node, Nelson Mandela University Ocean Sciences Campus, Gqeberha (Port Elizabeth), South Africa
| | - Mark de Bruyn
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia.,Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Simon Creer
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Gary Carvalho
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Marc Rius
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK.,Centre for Advanced Studies of Blanes (CEAB, CSIC), Accés a la Cala Sant Francesc 14, 17300 Blanes, Spain.,Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| |
Collapse
|
240
|
Korbel KL, Rutlidge H, Hose GC, Eberhard SM, Andersen MS. Dynamics of microbiotic patterns reveal surface water groundwater interactions in intermittent and perennial streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:152380. [PMID: 34914978 DOI: 10.1016/j.scitotenv.2021.152380] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/25/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Exchange between groundwater (GW), hyporheic zone waters (HZ) and surface waters (SW) is critical for water quality, quantity, and the ecological health and functioning of all three ecosystems. Hydrological exchange is particularly important in intermittent creeks, such as in the Murray Darling Basin, Australia, where stream reaches shift from losing to gaining depending on the volume of surface flows. In this study we used hydrochemistry to identify SW-GW exchange and combined this with eDNA data to analyse the response of eukaryote and prokaryote communities to differing flow conditions within intermittent and perennial stream reaches. Our study suggested that SW and GW microbial communities were only around 30% similar. Differences in microbiota between SW, HZ and GW habitats were driven by changes in relative abundances of surface water dominant organisms (such as those capable of photosynthesis) as well as anaerobic taxa typical of GW environments (e.g., methanogens), with GW and HZ microbial communities becoming increasingly different to those in SW as flow ceased in intermittent creeks. Fine-scale hydrologic changes were identified through microbial communities in the perennial Maules Creek, indicating the importance of GW-SW exchange to biotic communities. This study highlights the importance of flow in shaping microbial communities and biogeochemical cycling within intermittent creeks and their connected alluvial aquifers. Our results suggest that microbiota may prove a useful indicator of SW-GW exchange, and in some circumstances, may be more sensitive in demonstrating fine-scale changes in SW-GW interactions than water chemistry. This knowledge furthers our understanding of GW-SW exchange and its impacts on ecological health.
Collapse
Affiliation(s)
- K L Korbel
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia.
| | - H Rutlidge
- Water Research Laboratory, School of Civil & Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - G C Hose
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - S M Eberhard
- Subterranean Ecology Pty Ltd, Coningham, TAS 7054, Australia; Adjunct Affiliate University of New South Wales, Australia; Honorary Associate Western Australian Museum, Australia
| | - M S Andersen
- Water Research Laboratory, School of Civil & Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| |
Collapse
|
241
|
Evaluating eDNA for Use within Marine Environmental Impact Assessments. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10030375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this review, the use of environmental DNA (eDNA) within Environmental Impact Assessment (EIA) is evaluated. EIA documents provide information required by regulators to evaluate the potential impact of a development project. Currently eDNA is being incorporated into biodiversity assessments as a complementary method for detecting rare, endangered or invasive species. However, questions have been raised regarding the maturity of the field and the suitability of eDNA information as evidence for EIA. Several key issues are identified for eDNA information within a generic EIA framework for marine environments. First, it is challenging to define the sampling unit and optimal sampling strategy for eDNA with respect to the project area and potential impact receptor. Second, eDNA assay validation protocols are preliminary at this time. Third, there are statistical issues around the probability of obtaining both false positives (identification of taxa that are not present) and false negatives (non-detection of taxa that are present) in results. At a minimum, an EIA must quantify the uncertainty in presence/absence estimates by combining series of Bernoulli trials with ad hoc occupancy models. Finally, the fate and transport of DNA fragments is largely unknown in environmental systems. Shedding dynamics, biogeochemical and physical processes that influence DNA fragments must be better understood to be able to link an eDNA signal with the receptor’s state. The biggest challenge is that eDNA is a proxy for the receptor and not a direct measure of presence. Nonetheless, as more actors enter the field, technological solutions are likely to emerge for these issues. Environmental DNA already shows great promise for baseline descriptions of the presence of species surrounding a project and can aid in the identification of potential receptors for EIA monitoring using other methods.
Collapse
|
242
|
Câmara PEAS, Menezes GCA, Pinto OHB, Silva MC, Convey P, Rosa LH. Using metabarcoding to assess Viridiplantae sequence diversity present in Antarctic glacial ice. AN ACAD BRAS CIENC 2022; 94:e20201736. [PMID: 35239797 DOI: 10.1590/0001-3765202220201736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 06/04/2021] [Indexed: 11/22/2022] Open
Abstract
Antarctica contains most of the glacial ice on the planet, a habitat that is largely unexplored by biologists. Recent warming in parts of Antarctica, particularly the Antarctic Peninsula region, is leading to widespread glacial retreat, releasing melt water and, potentially, contained biological material and propagules. In this study, we used a DNA metabarcoding approach to characterize Viridiplantae DNA present in Antarctic glacial ice. Ice samples from six glaciers in the South Shetland Islands and Antarctic Peninsula were analysed, detecting the presence of DNA representing a total of 16 taxa including 11 Chlorophyta (green algae) and five Magnoliophyta (flowering plants). The green algae may indicate the presence of a viable algal community in the ice or simply of preserved DNA, and the sequence diversity assigned included representatives of Chlorophyta not previously recorded in Antarctica. The presence of flowering plant DNA is most likely to be associated with pollen or tissue fragments introduced by humans.
Collapse
Affiliation(s)
- Paulo E A S Câmara
- Universidade de Brasília, Departamento de Botânica, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, s/n, 70910-900 Brasília, DF, Brazil.,Universidade Federal de Santa Catarina, Pós-graduação em Plantas, Fungos e Algas, Campus Universitário, s/n, Sala 208, Bloco E, Córrego Grande, 88040-900 Florianópolis, SC, Brazil
| | - Graciele C A Menezes
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Av. Antônio Carlos, 6627, Pampulha, 31270-000 Belo Horizonte, MG, Brazil
| | - Otavio H B Pinto
- Universidade de Brasília, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, s/n, 70910-000 Brasília, DF, Brazil
| | - Micheline C Silva
- Universidade de Brasília, Departamento de Botânica, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, s/n, 70910-900 Brasília, DF, Brazil
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, U.K.,University of Johannesburg, Department of Zoology, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Luiz H Rosa
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Av. Antônio Carlos, 6627, Pampulha, 31270-000 Belo Horizonte, MG, Brazil
| |
Collapse
|
243
|
Verdier H, Konecny-Dupre L, Marquette C, Reveron H, Tadier S, Grémillard L, Barthès A, Datry T, Bouchez A, Lefébure T. Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers. Mol Ecol Resour 2022; 22:2158-2170. [PMID: 35218316 DOI: 10.1111/1755-0998.13604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022]
Abstract
The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as water filtration and DNA precipitation are time consuming, require difficult-to-handle equipment and partially integrate eDNA signals. To overcome these limitations, we created the first proof of concept of a passive, 3D-printed and easy-to-use eDNA sampler. We designed the samplers from hydroxyapatite (HAp samplers), a natural mineral with a high DNA adsorption capacity. The porous structure and shape of the samplers were designed to optimise DNA adsorption and facilitate their handling in the laboratory and in the field. Here we show that HAp samplers can efficiently collect genomic DNA in controlled set-ups, but can also collect animal eDNA under controlled and natural conditions with yields similar to conventional methods. However, we also observed large variations in the amount of DNA collected even under controlled conditions. A better understanding of the DNA-hydroxyapatite interactions on the surface of the samplers is now necessary to optimise the eDNA adsorption and to allow the development of a reliable, easy-to-use and reusable eDNA sampling tool.
Collapse
Affiliation(s)
- Héloïse Verdier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France.,Eurofins Hydrobiologie France, Rue Lucien Cuenot, 54521, Maxéville, France.,INRAE, UR-Riverly, Centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626, VILLEURBANNE Cedex, France
| | - Lara Konecny-Dupre
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
| | - Christophe Marquette
- 3d.FAB, Univ Lyon, Université Lyon1, CNRS, INSA, CPE-Lyon, ICBMS, UMR 5246, 43, Bd du 11 novembre 1918, 69622, Villeurbanne cedex, France
| | - Helen Reveron
- Univ Lyon, INSA Lyon, UCBL, CNRS, MATEIS UMR 5510, 69621, Villeurbanne, France
| | - Solène Tadier
- Univ Lyon, INSA Lyon, UCBL, CNRS, MATEIS UMR 5510, 69621, Villeurbanne, France
| | - Laurent Grémillard
- Univ Lyon, INSA Lyon, UCBL, CNRS, MATEIS UMR 5510, 69621, Villeurbanne, France
| | - Amélie Barthès
- Eurofins Hydrobiologie France, Rue Lucien Cuenot, 54521, Maxéville, France
| | - Thibault Datry
- INRAE, UR-Riverly, Centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626, VILLEURBANNE Cedex, France
| | - Agnès Bouchez
- INRAE, USMB, UMR CARRTEL, 75bis av. de Corzent, 742000, Thonon les Bains, France
| | - Tristan Lefébure
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
| |
Collapse
|
244
|
Sakata MK, Kawata MU, Kurabayashi A, Kurita T, Nakamura M, Shirako T, Kakehashi R, Nishikawa K, Hossman MY, Nishijima T, Kabamoto J, Miya M, Minamoto T. Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.76534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
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.
Collapse
|
245
|
Moss WE, Harper LR, Davis MA, Goldberg CS, Smith MM, Johnson PTJ. Navigating the trade‐offs between environmental
DNA
and conventional field surveys for improved amphibian monitoring. Ecosphere 2022. [DOI: 10.1002/ecs2.3941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Wynne E. Moss
- Department of Ecology & Evolutionary Biology University of Colorado Boulder Colorado USA
| | - Lynsey R. Harper
- Illinois Natural History Survey Prairie Research Institute, University of Illinois at Urbana‐Champaign Champaign Illinois USA
- NatureMetrics Ltd, CABI Site Egham UK
| | - Mark A. Davis
- Illinois Natural History Survey Prairie Research Institute, University of Illinois at Urbana‐Champaign Champaign Illinois USA
| | - Caren S. Goldberg
- School of the Environment Washington State University Pullman Washington USA
| | - Matthew M. Smith
- School of the Environment Washington State University Pullman Washington USA
| | - Pieter T. J. Johnson
- Department of Ecology & Evolutionary Biology University of Colorado Boulder Colorado USA
| |
Collapse
|
246
|
Zhang S, Zheng Y, Zhan A, Dong C, Zhao J, Yao M. Environmental DNA captures native and non-native fish community variations across the lentic and lotic systems of a megacity. SCIENCE ADVANCES 2022; 8:eabk0097. [PMID: 35148174 PMCID: PMC8836804 DOI: 10.1126/sciadv.abk0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Globally, urbanization poses a major threat to terrestrial biodiversity, yet its impact on fish diversity is poorly understood, mainly because of surveying difficulties. In this study, environmental DNA metabarcoding was used to survey fish communities at 109 lentic and lotic sites across Beijing, and how environmental variables affect fish biodiversity at fine urban spatial scales was investigated. We identified 52 native and 23 non-native taxa, with lentic and lotic waters harboring both common and habitat-specific species. Water quality strongly affected native fish diversity, especially in lentic systems, but had little influence on non-native diversity. Fish diversity showed little response to urban land cover variation, but the relative sequence abundance of non-natives in lotic waters increased linearly with distance from the city center. Our findings illustrate the complex effects of urbanization on native versus non-native fishes in different aquatic habitats and highlight the distinctive considerations needed to conserve urban aquatic biodiversity.
Collapse
Affiliation(s)
- Shan Zhang
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yitao Zheng
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Chunxia Dong
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
- Corresponding author. ,
| |
Collapse
|
247
|
Korbel KL, Greenfield P, Hose GC. Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150870. [PMID: 34627912 DOI: 10.1016/j.scitotenv.2021.150870] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/21/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.
Collapse
Affiliation(s)
- K L Korbel
- Department of Biological Sciences, Macquarie University, Australia.
| | | | - G C Hose
- Department of Biological Sciences, Macquarie University, Australia
| |
Collapse
|
248
|
Balech B, Sandionigi A, Marzano M, Pesole G, Santamaria M. MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences. Database (Oxford) 2022; 2022:6521297. [PMID: 35134858 PMCID: PMC9216479 DOI: 10.1093/database/baab084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 01/05/2023]
Abstract
Nucleotide sequences reference collections or databases are fundamental components in DNA barcoding and metabarcoding data analyses pipelines. In such analyses, the accurate taxonomic assignment is a crucial aspect, relying directly on the availability of comprehensive and curated reference sequence collection and its taxonomy information. The currently wide use of the mitochondrial cytochrome oxidase subunit-I (COXI) as a standard DNA barcode marker in metazoan biodiversity studies highlights the need to shed light on the availability of the related relevant information from different data sources and their eventual integration. To adequately address data integration process, many aspects should be markedly considered starting from DNA sequence curation followed by taxonomy alignment with solid reference backbone and metadata harmonization according to universal standards. Here, we present MetaCOXI, an integrated collection of curated metazoan COXI DNA sequences with their associated harmonized taxonomy and metadata. This collection was built on the two most extensive available data resources, namely the European Nucleotide Archive (ENA) and the Barcode of Life Data System (BOLD). The current release contains more than 5.6 million entries (39.1% unique to BOLD, 3.6% unique to ENA, and 57.2% shared between both), their related taxonomic classification based on NCBI reference taxonomy, and their available main metadata relevant to environmental DNA studies, such as geographical coordinates, sampling country and host species. MetaCOXI is available in standard universal formats (‘fasta’ for sequences & ‘tsv’ for taxonomy and metadata), which can be easily incorporated in standard or specific DNA barcoding and/or metabarcoding data analysis pipelines. Database URL: https://github.com/bachob5/MetaCOXI
Collapse
Affiliation(s)
- Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, via Amendola 122/O, Bari 70126, Italy
| | - Anna Sandionigi
- Research and Development Department, Quantia Consulting srl, via Francesco Petrarca 20, Mariano Comense 22066, Italy
| | - Marinella Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, via Amendola 122/O, Bari 70126, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, via Amendola 122/O, Bari 70126, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari ‘A. Moro’, via Orabona 4, Bari 70126, Italy
| | - Monica Santamaria
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, via Amendola 122/O, Bari 70126, Italy
| |
Collapse
|
249
|
Young MR, Hebert PDN. Unearthing soil arthropod diversity through DNA metabarcoding. PeerJ 2022; 10:e12845. [PMID: 35178296 PMCID: PMC8815377 DOI: 10.7717/peerj.12845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/06/2022] [Indexed: 01/10/2023] Open
Abstract
DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna-the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.
Collapse
Affiliation(s)
- Monica R. Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
250
|
Maduna SN, Vivian-Smith A, Jónsdóttir ÓDB, Imsland AK, Klütsch CF, Nyman T, Eiken HG, Hagen SB. Mitogenomics of the suborder Cottoidei (Teleostei: Perciformes): Improved assemblies, mitogenome features, phylogeny, and ecological implications. Genomics 2022; 114:110297. [DOI: 10.1016/j.ygeno.2022.110297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 01/05/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
|