Article
Geography, Physical
A. T. M. ter Schure, M. Bajard, K. Loftsgarden, H. Hoeg, E. Ballo, J. Bakke, E. W. N. Storen, F. Iversen, A. Kool, A. K. Brysting, K. Kruger, S. Boessenkool
Summary: By integrating interdisciplinary analyses of long-term records, this study uncovers the anthropogenic and environmental drivers behind vegetation dynamics in southeastern Norway during the Holocene period. The combined analysis of pollen, sedaDNA, geochemical, and archaeological data reveals consistent vegetation signals and agricultural intensification over the past 10,000 years. The study provides insights into the effects of human land-use and environmental changes on vegetation dynamics in the region.
QUATERNARY SCIENCE REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Joanne E. Littlefair, Michael D. Rennie, Melania E. Cristescu
Summary: This study evaluates the potential of environmental RNA (eRNA) released by macroeukaryotes as a biomonitoring tool. The results show that eRNA can be filtered from water and reliably provide species composition information through metabarcoding analysis. Compared to eDNA, eRNA has a higher true positive rate, making it a promising addition to the suite of molecular monitoring tools.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Medicine, Legal
Nicole R. Foster, Belinda Martin, Jurian Hoogewerff, Michael G. Aberle, Patrice de Caritat, Paul Roffey, Robert Edwards, Arif Malik, Priscilla Thwaites, Michelle Waycott, Jennifer Young
Summary: Environmental DNA and elemental and mineralogical analysis of soil can be used in forensic intelligence work by analyzing the airborne fraction of soil (dust). Massive parallel sequencing technologies enable the identification of genetic fingerprints in dust particles. Combining this with elemental and mineralogical compositions offers multiple lines of evidence for tracing the origin of dust samples.
FORENSIC SCIENCE INTERNATIONAL
(2023)
Article
Engineering, Environmental
Armin Kavehei, Grant C. Hose, Anthony A. Chariton, Damian B. Gore
Summary: The study used environmental (e)DNA metabarcoding to assess the impacts of metal contaminants on biota downstream of a legacy base metal sulfide mine in southeastern Australia. Although metal concentrations were relatively low, biological communities in sediment samples showed impacts indicating the effectiveness of metabarcoding in capturing the sensitivities of a diverse range of organisms and providing a more ecological robust perspective on the downstream effects of legacy mines.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Biodiversity Conservation
Kaede Miyata, Yasuaki Inoue, Yuto Amano, Tohru Nishioka, Masayuki Yamane, Takamitsu Kawaguchi, Osamu Morita, Hiroshi Honda
Summary: This study found that there are sufficient amounts of eRNA in water samples from rivers in Japan to support ecological surveys based on eRNA, with higher correlation and positive predictivity compared to eDNA.
ECOLOGICAL INDICATORS
(2021)
Article
Engineering, Environmental
Armin Kavehei, Damian B. Gore, Anthony A. Chariton, Grant C. Hose
Summary: This study investigated the environmental impacts of two legacy metal mines discharge metals into a creek, using sediment and water chemistry coupled with eDNA metabarcoding. The results showed that the Peelwood copper mine was the main source of contamination for Peelwood Creek, and prokaryotes were found to be good indicators of metal contamination.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Environmental Sciences
Armin Kavehei, Damian B. Gore, Anthony A. Chariton, Grant C. Hose
Summary: The study investigated the spatial distribution of biota and soil chemistry data in surface soil from Sunny Corner, Australia, a legacy base metal sulfide mine. Results indicated that copper, zinc, arsenic, and lead in the surface soil exceeded Australian national soil quality guidelines, posing risks to the environment. Environmental DNA metabarcoding of prokaryote and eukaryote composition confirmed these risks, suggesting its potential for rapid ecological assessment of contaminated sites.
Article
Engineering, Environmental
Kyu-Young Shim, Heesang Shin, In-Cheol Yeo, Kyu Ri Kim, Ihn-Sil Kwak, Chang Bum Jeong
Summary: In this study, environmental DNA (eDNA) metabarcoding was used to monitor invertebrate outbreaks at different stages of drinking water treatment. The composition of invertebrate eDNA communities reflected the source water communities in earlier stages, but some dominant taxa were introduced during purification and eliminated in later stages. The study also assessed the detection/quantification limits and read capacity of eDNA metabarcoding for biocontamination surveillance in drinking water treatment plants (DWTPs). A novel eDNA-based approach for sensitive and efficient surveillance of invertebrate outbreaks in DWTPs was proposed.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Microbiology
Liisi Talas, Normunds Stivrins, Siim Veski, Leho Tedersoo, Veljo Kisand
Summary: The study reveals the diversity and changes in fungal communities in lake sediments throughout the Holocene period. It shows that plankton parasitic fungi became more diverse in the last few millennia, potentially in response to a cooler climate. Major shifts in fungal communities, particularly in plankton parasites and mycorrhizal fungi, occurred during the Late Holocene and Latest Holocene periods, possibly influenced by increased transfer rates of plant material and human impact.
Article
Environmental Sciences
Sinziana F. Rivera, Valentin Vasselon, Nathalie Mary, Olivier Monnier, Frederic Rimet, Agnes Bouchez
Summary: Recent studies suggest that aquatic biofilms can physically act as sorptive sponges of DNA. By using biofilm samples for DNA collection, both ecological assessment and higher diversity for certain organisms can be detected, which are challenging to achieve with morphological methods.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Mahsa Mousavi-Derazmahalleh, Audrey Stott, Rose Lines, Georgia Peverley, Georgia Nester, Tiffany Simpson, Michal Zawierta, Marco De la Pierre, Michael Bunce, Claus T. Christophersen
Summary: Metabarcoding of environmental DNA (eDNA) with high throughput sequencing is transforming biodiversity monitoring, but the multitude of bioinformatic tools poses challenges. The eDNAFlow pipeline, utilizing Nextflow and Singularity, offers an automated workflow for scalable, portable, and reproducible data processing. Demonstrated utility and efficiency in coral diversity biomonitoring study and scalability with large data set analysis.
MOLECULAR ECOLOGY RESOURCES
(2021)
Review
Genetics & Heredity
Toshifumi Minamoto
Summary: In an era of severe biodiversity loss, biological monitoring is becoming increasingly important. The analysis of environmental DNA (eDNA) has emerged as a new method that can revolutionize the monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has made significant progress and is quickly becoming the preferred method for non-destructive and non-invasive biological monitoring. This review summarizes the development and techniques of macro-organismal eDNA analysis, and discusses the future prospects of combining these methods with advanced analytical techniques in the fields of molecular biology and molecular genetics.
Article
Environmental Sciences
Marissa S. Giroux, Jay R. Reichman, Troy Langknecht, Robert M. Burgess, Kay T. Ho
Summary: This study investigated the effects of nanoplastics on benthic micro- and meiofaunal community diversity using a metabarcoding approach. The results showed that the highest concentration of nanoplastics exposure led to increased diversity and significant changes in community composition, driven by differential abundance of specific protists and arthropods.
ENVIRONMENTAL POLLUTION
(2023)
Article
Ecology
Elizabeth Andruszkiewicz Allan, Ryan P. Kelly, Erin R. D'Agnese, Maya N. Garber-Yonts, Megan R. Shaffer, Zachary J. Gold, Andrew O. Shelton
Summary: Environmental laws worldwide require environmental impact assessments for construction projects and human development. The use of environmental DNA (eDNA) analysis through amplification sequencing provides a powerful and effective method for analyzing the biological elements of ecosystems in these assessments. This study utilized eDNA to estimate absolute concentrations of multiple species in a freshwater stream before and after culvert removal, revealing the impact of this environmental intervention on salmonid populations.
ECOLOGICAL APPLICATIONS
(2023)
Article
Medicine, Legal
Yanlei Liu, Chao Xu, Wenpan Dong, Xueying Yang, Shiliang Zhou
Summary: This study demonstrates how environmental plant DNA metabarcoding technology was used to determine a criminal suspect. By extracting DNA, amplifying genes, sequencing, and bioinformatics analysis, the suspect was successfully identified. This indicates that plant DNA in environmental soil can be a new source of evidence with high potentials for applications in criminal cases.
FORENSIC SCIENCE INTERNATIONAL
(2021)
Article
Ecology
Georgia Thomson-Laing, Jamie D. Howarth, Marcus J. Vandergoes, Susanna A. Wood
Summary: Monitoring fish populations is crucial for understanding their dynamics and conservation efforts. This study focuses on finding the most effective method for extracting fish DNA from lake-surface sediments, using eel and perch as target genes. Two optimized methods are recommended, with the Lakes ABPS protocol being a cheaper and more automated option.
FRESHWATER BIOLOGY
(2022)
Article
Geography, Physical
Joseph G. Prebble, Gavin Dunbar, Valerie van den Bos, Xun Li, Marcus Vandergoes, Sarah Richardson, Huw Horgan, Katherine A. Holt, Jamie Howarth, Richard Levy
Summary: This study explores the potential for generating long proxy records of tree mast seeding using pollen deposited in lake sediments and reconstructs masting events for two genera of Southern Beech. The results show that the pollen records reflect the mast frequency changes and demonstrate the potential of using long records to enhance our understanding of the environmental drivers of mast seeding.
Article
Geology
Bruce W. Hayward, Ashwaq T. Sabaa, Jamie D. Howarth, Alan R. Orpin, Lorna J. Strachan
Summary: The 2016 Kaikoura Earthquake triggered large-scale turbidity currents, and the study found that the source and flow history of these currents can be determined by the relative abundance of benthic genera, the planktic foraminiferal index, the absolute test abundance, and the planktic percentage of foraminiferal faunas.
NEW ZEALAND JOURNAL OF GEOLOGY AND GEOPHYSICS
(2022)
Article
Limnology
John K. Pearman, Janet Adamson, Georgia Thomson-Laing, Lucy Thompson, Sean Waters, Marcus J. Vandergoes, Jamie D. Howarth, Susanna A. Wood
Summary: Biological communities in lake surface sediments are crucial for biogeochemical cycling and ecosystem services. This study investigated abundance-occupancy patterns and assembly processes of bacteria and eukaryotes across a large spatial scale and multiple environmental gradients. The results provide new insights into the ecology of these organisms and the effects of environmental stressors on lake sediment communities.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Geochemistry & Geophysics
Sean Waters, Javier Atalah, Lucy Thompson, Georgia Thomson-Laing, John K. Pearman, Jonathan Puddick, Jamie D. Howarth, Lizette Reyes, Marcus J. Vandergoes, Susanna A. Wood
Summary: Lake ecosystems worldwide are experiencing eutrophication and degradation due to human activities. Limited data hinders the understanding of lake health at national scales, making long-term monitoring impractical. Analyzing sediment geochemistry provides an efficient method for assessing contemporary water quality and predicting trophic levels in unmonitored lakes.
APPLIED GEOCHEMISTRY
(2023)
Article
Geography, Physical
Charlotte O. Pizer, Jamie D. Howarth, Kate J. Clark, Colin J. N. Wilson, Stephanie E. Tickle, Jenni L. Hopkins, Jenny A. Dahl
Summary: Volcanic ash (tephra) horizons are important for correlating natural archives, but age uncertainties can hinder their effectiveness. We use the Waimihia tephra as a case study to improve age constraints for Holocene tephra isochrons by employing detailed assessments, precise AMS dating, and Bayesian age models. Our findings have implications for refining paleoearthquake correlations and chronologies relying on the Waimihia isochron.
QUATERNARY SCIENCE REVIEWS
(2023)
Article
Environmental Sciences
Rose Gregersen, Jamie D. Howarth, Javier Atalah, John K. Pearman, Sean Waters, Xun Li, Marcus J. Vandergoes, Susanna A. Wood
Summary: Lakes are important for ecosystem services and biodiversity, but cultural eutrophication remains a major threat to their health. The lack of long-term monitoring records limits our ability to manage lake eutrophication. This study developed a bio-indicator approach using diatom communities to infer trophic levels in lakes, and the results were consistent with monitoring data and land-use histories. However, recent shifts in diatom communities were not captured by traditional trophic level indices, highlighting the importance of new approaches in preventing the decline of lake ecosystems worldwide.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biology
Georgia Thomson-Laing, Lena Schallenberg, David Kelly, Jamie D. Howarth, Susanna A. Wood
Summary: Freshwater fish are facing a perilous situation, as more than 30% of species are critically endangered. However, determining the impact of disturbances on native fish communities is challenging due to ecological and methodological complexities. This review examines current methods used to assess the responses of fish communities, particularly in lakes, and identifies knowledge gaps and challenges. The authors advocate for an integrative approach that combines emerging technologies and underutilized knowledge streams, alongside conventional methods, to enable more informed and effective management actions.
BIOLOGICAL REVIEWS
(2023)
Article
Marine & Freshwater Biology
Jonathan Puddick, Sebastian Naeher, John K. Pearman, Carrie D. Page, Donato Romanazzi, Lena A. Schallenberg, Jamie D. Howarth, Marcus J. Vandergoes, Susanna A. Wood
Summary: Cyanobacterial blooms are increasing globally, impacting lake ecosystems and posing a risk to human and animal health. Cyanobacterial pigments preserved in lake sediments can help understand the changes that have led to these blooms. By analyzing pigments in cyanobacteria cultures and applying the findings to lake sediments, we found that carotenoids can be used to evaluate cyanobacterial abundance and differentiate different cyanobacteria types. Ratios of specific carotenoids can be used as a proxy to evaluate historical shifts in cyanobacterial communities.
Article
Environmental Sciences
Rose Gregersen, John K. Pearman, Javier Atalah, Sean Waters, Marcus J. Vandergoes, Jamie D. Howarth, Georgia Thomson-Laing, Lucy Thompson, Susanna A. Wood
Summary: Anthropogenic eutrophication, a pressing issue for lakes globally, is difficult to manage due to limited monitoring records. This study presents a taxonomy-free diatom-based biomonitoring method using environmental DNA metabarcoding data, offering an accurate and automated alternative for eutrophication monitoring.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Limnology
Susanna A. Wood, Marcus J. Vandergoes, Javier Atalah, Jamie D. Howarth, Sean Waters, Georgia Thomson-Laing, Lucy Thompson, David P. Hamilton, Xavier Pochon, David Kelly, Chris Moy, Andrew Rees, Marc Schalleberg, Rose Gregerson, Adelaine Moody, Lizette Reyes, Claire Shepherd, Henry Gard, Lisa Floerl, John K. Pearman
Summary: Pressure on lakes in Aotearoa New Zealand is increasing due to elevated catchment nutrient loads, establishment of non-native species, and climate change. This study predicts the trophic status of lakes at a national scale and identifies lakes that should be prioritized for protection to prevent further degradation.