Article
Multidisciplinary Sciences
Zeshu Yu, Shin-ichi Ito, Marty Kwok-Shing Wong, Susumu Yoshizawa, Jun Inoue, Sachihiko Itoh, Ryuji Yukami, Kazuo Ishikawa, Chenying Guo, Minoru Ijichi, Susumu Hyodo
Summary: In this study, the performance of two OceanDNA analysis methods, qPCR and MiFish, were tested to determine the distribution of small pelagic fish in the open ocean. The results showed a positive correlation between the two methods, but the detection rate using qPCR was consistently higher than that of MiFish. It was recommended to use both methods together to monitor the quantitative distribution and fish community structures of small pelagic fish species.
Article
Multidisciplinary Sciences
Kinuyo Yoneya, Masayuki Ushio, Takeshi Miki
Summary: A reliable survey method called plant flow collection, using environmental DNA (eDNA) metabarcoding, was developed to address the challenges in collecting and identifying terrestrial arthropods. By extracting DNA from water collected on the surface of plants, a high-throughput sequencing platform was used to identify various arthropods at the family level. The results showed that this method could detect arthropod eDNA that was not observed in visual surveys, demonstrating its potential for efficient and comprehensive surveys.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Lynne M. Christianson, Shannon B. Johnson, Darrin T. Schultz, Steven H. D. Haddock
Summary: Despite historical difficulties in studying ctenophores, new primers have successfully amplified COI fragments, highlighting high diversity and supporting ecological and morphological differences among species. These new tools provide important advancements for researchers in exploring ctenophore diversity on a global scale.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Environmental Sciences
Peter A. U. Staehr, Karsten Dahl, Helle Buur, Cordula Goeke, Rumakanta Sapkota, Anne Winding, Marina Panova, Matthias Obst, Per Sundberg
Summary: This study investigated the use of eDNA metabarcoding as a supplement to traditional diver-based monitoring of marine boulder reef biodiversity within the photic zone. The results showed that eDNA sampling provided a substantial supplement to traditional monitoring, despite a low detection of macroalgae. This suggests that eDNA methods should be added to conventional monitoring programs in the future.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Zachary Gold, Emily E. Curd, Kelly D. Goodwin, Emma S. Choi, Benjamin W. Frable, Andrew R. Thompson, Harold J. Walker, Ronald S. Burton, Dovi Kacev, Lucas D. Martz, Paul H. Barber
Summary: This study evaluates the performance of DNA metabarcoding in classifying fish species in the California Current Large Marine Ecosystem. It shows that a regional database provides higher accuracy than a global one, and highlights the tradeoff between accuracy and misclassification when setting taxonomic cutoff scores. Additionally, adding new reference sequences improves the identification of native species in environmental DNA samples, emphasizing the importance of curated reference databases for effective metabarcoding.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Joeselle Serrana, Kozo Watanabe
Summary: Metabarcoding is a fast and cost-effective tool for species identification, and this study assessed its ability to infer haplotypes in freshwater macroinvertebrates. The influence of DNA template concentration and PCR cycle on detecting true and false haplotypes was also examined.
Article
Marine & Freshwater Biology
Vincent Prie, Alice Valentini, Manuel Lopes-Lima, Elsa Froufe, Mathieu Rode, Nicolas Poulet, Pierre Taberlet, Tony Dejean
Summary: The study introduces a metabarcoding approach for freshwater bivalves, which has been shown to be more effective in detecting a greater number of species compared to traditional methods. The developed primers have been proven to be effective globally, providing a new tool for freshwater bivalve monitoring worldwide.
Review
Environmental Sciences
Sergio Ramirez-Amaro, Marta Bassitta, Antonia Picornell, Cori Ramon, Barbara Terrasa
Summary: Fisheries management involves complex tasks, and monitoring fishing activities is challenging. The emerging molecular method of environmental DNA (eDNA) has the potential to provide unique understanding of ecological processes in marine environments and improve fisheries monitoring. Many studies suggest that eDNA has the potential to revolutionize fisheries assessment.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Fisheries
Simone D'Alessandro, Stefano Mariani
Summary: Marine ecosystems are rapidly changing due to various anthropogenic impacts, leading to disruptions in productivity dynamics and alterations in marine food webs. Traditional methods for surveying marine food webs are laborious and costly, but a new low-cost approach using environmental DNA analysis shows promise in providing rapid and scalable monitoring of ecosystem structure.
FISH AND FISHERIES
(2021)
Review
Geochemistry & Geophysics
Masaki Miya
Summary: This article reviews the application of eDNA metabarcoding in monitoring marine fish communities and discusses its prospects in biodiversity monitoring. eDNA metabarcoding can predict species richness, detect habitat segregation and biogeographic patterns, and monitor the dynamics of fish communities. It can also assess the impact of human activities on fish communities.
ANNUAL REVIEW OF MARINE SCIENCE
(2022)
Article
Biodiversity Conservation
M. Laporte, C. S. Berger, E. Garcia-Machado, G. Cote, O. Morissette, L. Bernatchez
Summary: The study found that the use of environmental DNA (eDNA) metabarcoding can accurately assess the composition and spatial distribution of freshwater fish communities. In a transplant experiment in the St. Lawrence River, the eDNA of brown trout was detected at five locations up to 5,000 meters from the cage, but only one sampling location downstream from the cage showed a significant impact on community composition. Cluster analysis confirmed the impact of the brown trout eDNA on community composition, separating this location from others. No evidence of transport effect of brown trout eDNA on fish community composition was observed in other sampling locations.
ECOLOGICAL INDICATORS
(2022)
Article
Fisheries
Clare I. M. Adams, Gert-Jan Jeunen, Hugh Cross, Helen R. Taylor, Antoine Bagnaro, Kim Currie, Chris Hepburn, Neil J. Gemmell, Lara Urban, Federico Baltar, Michael Stat, Michael Bunce, Michael Knapp
Summary: In response to climate change, efficient monitoring methods are needed for rapidly shifting biodiversity patterns in the oceans. Environmental DNA (eDNA) metabarcoding has emerged as a cost-effective solution. Using eDNA, we detected four community types across a transect in the Southern Hemisphere and found that diversity patterns were mainly driven by planktonic organisms. This technique lays the foundations for multi-trophic environmental monitoring efforts.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Environmental Sciences
Rose Lines, Manjeeti Juggernauth, Georgia Peverley, James Keating, Tiffany Simpson, Mahsa Mousavi-Derazmahalleh, Michael Bunce, Alice Taysom, Angelo F. Bernardino, Phillip Whittle
Summary: This study conducted a large-scale eDNA monitoring of marine vertebrates in coastal waters of Brazil, using metabarcoding assays. The results revealed temporal and spatial differences in the biodiversity of marine vertebrates. The study reinforces the importance of monitoring coastal environments and understanding the impacts of human activities through the collection of time-stamped environmental samples.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
Laura L. Hauck, Carla L. Atkinson, Jessica A. Homyack, Brooke E. Penaluna, Clay Mangum, Ashley A. Coble, Jami Nettles, Jamie E. Thornton-Frost, Miranda J. Fix
Summary: The use of environmental DNA (eDNA) has great potential for monitoring and managing threatened species, such as freshwater mussels. However, challenges exist in accurately describing the full suite of species present, especially in diverse freshwater mussel populations. This study developed a microfluidic metabarcoding array to target a wide range of species and compared eDNA surveys with traditional quadrat surveys to assess mussel species diversity.
Article
Biodiversity Conservation
Martina Vasutova, Martin Jirousek, Michal Hajek
Summary: The study revealed that fungal communities in boreal ecosystems are primarily influenced by substrate identity rather than site differences. Only a few fungi behave as generalists across different plant species, while most specific fungi are found in dead parts of specific plants.
ECOLOGICAL INDICATORS
(2021)
Article
Ecology
Kristen Fernandes, Mieke van der Heyde, Megan Coghlan, Grant Wardell-Johnson, Michael Bunce, Richard Harris, Paul Nevill
RESTORATION ECOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Mieke van der Heyde, Michael Bunce, Grant Wardell-Johnson, Kristen Fernandes, Nicole E. White, Paul Nevill
MOLECULAR ECOLOGY RESOURCES
(2020)
Article
Multidisciplinary Sciences
Miwa Takahashi, Joseph D. DiBattista, Simon Jarman, Stephen J. Newman, Corey B. Wakefield, Euan S. Harvey, Michael Bunce
SCIENTIFIC REPORTS
(2020)
Article
Environmental Sciences
R. D. Evans, K. M. McMahon, K-J Van Dijk, K. Dawkins, M. Nilsson Jacobi, A. Vikrant
Summary: Seagrasses are important habitats providing ecological services, but limited understanding exists on dispersal distances of species like Halodule uninervis. Research suggests that despite fragment viability of up to 28 days, dispersal of H. uninervis is spatially limited by factors such as oceanographic features and habitat continuity.
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)
Article
Biochemistry & Molecular Biology
Mieke van der Heyde, Michael Bunce, Kingsley W. Dixon, Kristen Fernandes, Jonathan Majer, Grant Wardell-Johnson, Nicole E. White, Paul Nevill
Summary: Invertebrates play a crucial role in restoration processes, but often overlooked due to their diversity and the difficulties in surveying and identification. DNA metabarcoding is a useful tool to rapidly survey invertebrate communities and understand their interactions with other taxa. This study evaluated the changes in invertebrate communities during mine-site restoration using DNA metabarcoding. It was found that ground-dwelling invertebrates showed clearer restoration signals compared to airborne invertebrates, with the inclusion of plant assays providing additional information about the restoration process.
Article
Ecology
Kristen Fernandes, Kit Prendergast, Philip W. Bateman, Benjamin J. Saunders, Mark Gibberd, Michael Bunce, Paul Nevill
Summary: Urbanisation has complex effects on the foraging behavior of native bees, with oligolectic bee species showing higher diversity of plant pollen in residential gardens, while the diversity and composition of plant forage in polylectic bee nesting tubes did not vary between habitat types.
Article
Biodiversity Conservation
Kristen Fernandes, Philip W. Bateman, Benjamin J. Saunders, Michael Bunce, Kristine Bohmann, Paul Nevill
Summary: Severely fragmented habitats increase the risk of extirpation of native mammal populations. In this study, metabarcoding of invertebrate-derived DNA (iDNA) from carrion flies was used to track mammal populations in an anthropogenically altered landscape. The results showed that the signals from iDNA reflected the known distribution of target mammals in the region. iDNA metabarcoding has potential for noninvasive monitoring of mammals and informing conservation decision-making.
CONSERVATION BIOLOGY
(2023)
Article
Environmental Sciences
M. Mousavi-Derazmahalleh, R. J. Ellis, B. L. D'Rozario, T. E. Berry, G. Peverley, K. L. Dawkins, M. Campbell, N. E. White, M. E. Allentoft
Summary: Environmental DNA (eDNA) research is revolutionizing global biomonitoring, but its effectiveness for reptiles has been limited due to their low shedding rate. This study investigates whether targeting specific substrates can improve the detection of reptile eDNA, focusing on the rare and elusive Pilbara olive python. By analyzing water samples from rock pools, the presence of Pilbara olive python eDNA was confirmed, suggesting the potential for using eDNA-based methods for precision monitoring of this species.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Article
Fisheries
Miwa Takahashi, Corey B. Wakefield, Stephen J. Newman, Kyle B. Hillcoat, Benjamin J. Saunders, Euan S. Harvey
Summary: This study aimed to validate a robust and cost-effective method to discriminate the cryptic juveniles of sympatric red snappers using body and/or otolith morphometric data in a multivariate analysis. The most parsimonious multivariate models achieved accurate species prediction rates of 98.8%, which consisted of just three body variables. The method outlined in this study could be applied to distinguish other cryptic congeneric fish species, including from archived otolith collections.
JOURNAL OF FISH BIOLOGY
(2023)
Article
Marine & Freshwater Biology
Kathryn L. Dawkins, James M. Furse, Jane M. Hughes
Summary: Research on the biogeographic history of mesic Australian fauna with Gondwanan origins is limited. This study focused on the burrowing clade of Australian freshwater crayfish to analyze their origin, distribution, and diversification patterns. The results suggest that the clade originated during the early fragmentation of Gondwana in southern Australia, with divergence between extant taxa likely a result of both short- and long-distance dispersal events, influenced by fluctuating sea levels and changing climate into the Eocene.
Article
Environmental Sciences
Toshimi Nakajima, Mao Kuragano, Makoto Yamada, Ryo Sugimoto
Summary: This study compared the contribution of submarine groundwater discharge (SGD) to river nutrient budgets at nearshore and embayment scales, and found that SGD-derived nutrients become more important at larger spatial scales.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Fan Liu, Lei Zhang, Chongyang Zhang, Ziguang Chen, Jingguang Li
Summary: NO2 emissions from wall-mounted gas stoves used for household heating have become a significant source of indoor pollution in Chinese urban areas. The high indoor concentration of NO2 poses potential health risks to residents. It is urgently necessary to establish relevant regulations and implement emission reduction technologies to reduce NO2 emissions from wall-mounted gas stoves.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Letter
Environmental Sciences
Hans Peter H. Arp, Raoul Wolf, Sarah E. Hale, Sivani Baskaran, Juliane Gluege, Martin Scheringer, Xenia Trier, Ian T. Cousins, Harrie Timmer, Roberta Hofman-Caris, Anna Lennquist, Andre D. Bannink, Gerard J. Stroomberg, Rosa M. A. Sjerps, Rosa Montes, Rosario Rodil, Jose Benito Quintana, Daniel Zahn, Herve Gallard, Tobias Mohr, Ivo Schliebner, Michael Neumann
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Philomina Onyedikachi Peter, Binessi Edouard Ifon, Francois Nkinahamira, Kayode Hassan Lasisi, Jiangwei Li, Anyi Hu, Chang-Ping Yu
Summary: This study investigates the relationship between dissolved organic matter (DOM) and Rare Earth Elements (REEs) in sediments from Yundang Lagoon, China. The results show four distinct fluorescent components, with protein-like substances being the most prevalent. Additionally, the total fluorescence intensity and LREE concentrations exhibit a synchronized increase from Outer to Inner to Songbai Lake core sediments. The findings demonstrate a strong correlation between DOM content and pollution levels.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Surya Gupta, Pasquale Borrelli, Panos Panagos, Christine Alewell
Summary: The objective of this study is to incorporate soil hydraulic properties into the erodibility factor (K) of USLE-type models. By modifying and improving the existing equations for soil texture and permeability, the study successfully included information on saturated hydraulic conductivity (Ksat) into the calculation of K factor. Using the Random Forest machine learning algorithm, two independent K factor maps with different spatial resolutions were generated. The results show that the decrease in K factor values has a positive impact on the modeling of soil erosion rates.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Jesmin Akter, Wendy J. M. Smith, Yawen Liu, Ilho Kim, Stuart L. Simpson, Phong Thai, Asja Korajkic, Warish Ahmed
Summary: The choice of workflow in wastewater surveillance has a significant impact on SARS-CoV-2 concentrations, while having minimal effects on HF183 and no effect on HAdV 40/41 concentrations. Certain components in the workflow can be interchangeable, but factors such as buffer type, chloroform, and homogenization speed can affect the recovery of viruses and bacteria.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Yu Luo, Xueting Yang, Diwei Wang, Hongmei Xu, Hongai Zhang, Shasha Huang, Qiyuan Wang, Ningning Zhang, Junji Cao, Zhenxing Shen
Summary: Atmospheric PM2.5, which can generate reactive oxygen species (ROS), is associated with cardiorespiratory morbidity and mortality. The study found that both the mass concentration of PM2.5 and the DTT activity were higher during the heating season than during the nonheating season. Combustion sources were the primary contributors to DTT activity during the heating season, while secondary formation dominated during the nonheating season. The study also revealed that biomass burning had the highest inherent oxidation potential among all sources investigated.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Erin L. Murphy, Leah R. Gerber, Chelsea M. Rochman, Beth Polidoro
Summary: Plastic pollution has devastating consequences for marine organisms. This study uses a trait-based framework to develop a vulnerability index for marine mammals, seabirds, and sea turtles in Hawai'i. The index ranks 63 study species based on their vulnerability to macroplastic pollution, providing valuable information for species monitoring and management priorities.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Kenji Maurice, Amelia Bourceret, Sami Youssef, Stephane Boivin, Liam Laurent-Webb, Coraline Damasio, Hassan Boukcim, Marc-Andre Selosse, Marc Ducousso
Summary: Growing pressure from climate change and agricultural land use is destabilizing soil microbial community interactions. Little is known about microbial community resistance and adaptation to disturbances, hindering our understanding of recovery latency and implications for ecosystem functioning. This study found that anthropic disturbance and natural disturbance have different effects on the topology and stability of soil microbial networks.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Yunhao Li, Yali Feng, Haoran Li, Yisong Yao, Chenglong Xu, Jinrong Ju, Ruiyu Ma, Haoyu Wang, Shiwei Jiang
Summary: Deep-sea mining poses a serious threat to marine ecosystems and human health by disturbing sediment and transmitting metal ions through the food chain. This study developed a new regenerative adsorption material, OMN@SA, which effectively removes metal ions. The adsorption mechanism and performance of the material for metal ion fixation were investigated.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Antonio Medici, Margherita Lavorgna, Marina Isidori, Chiara Russo, Elena Orlo, Giovanni Luongo, Giovanni Di Fabio, Armando Zarrelli
Summary: Valsartan, a widely used antihypertensive drug, has been detected in high concentrations in surface waters due to its unchanged excretion and incomplete degradation in wastewater treatment plants. This study investigated the degradation of valsartan and identified 14 degradation byproducts. The acute and chronic toxicity of these byproducts were evaluated in key organisms in the freshwater trophic chain.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Jiang Lin, Lianbao Chi, Qing Yuan, Busu Li, Mingbao Feng
Summary: This study investigated the photodegradation behavior and product formation of two representative pharmaceuticals in simulated estuary water. The study found that the formed transformation products of these pharmaceuticals have potential toxicity on marine organisms, including oxidative stress and damage to cellular components.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Hua Fang, Dongdong Jiang, Ye He, Siyi Wu, Yuehong Li, Ziqi Zhang, Haoting Chen, Zixin Zheng, Yan Sun, Wenxiang Wang
Summary: This study revealed that exposure to lower levels of air pollutants led to decreased pregnancy rates, with PM10, NO2, SO2, and CO emerging as the four most prominent pollutants. Individuals aged 35 and above exhibited heightened susceptibility to pollutants.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Ali Shaan Manzoor Ghumman, Rashid Shamsuddin, Amin Abbasi, Mohaira Ahmad, Yoshiaki Yoshida, Abdul Sami, Hamad Almohamadi
Summary: In this study, inverse vulcanized polysulfides (IVP) were synthesized by reacting molten sulfur with 4-vinyl benzyl chloride, and then functionalized using N-methyl D-glucamine (NMDG). The functionalized IVP showed a high mercury adsorption capacity and a machine learning model was developed to predict the amount of mercury removed. Furthermore, the functionalized IVP can be regenerated and reused, providing a sustainable and cost-effective adsorbent.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Environmental Sciences
Rita Bonfiglio, Renata Sisto, Stefano Casciardi, Valeria Palumbo, Maria Paola Scioli, Erica Giacobbi, Francesca Servadei, Gerry Melino, Alessandro Mauriello, Manuel Scimeca
Summary: This study investigated the presence of aluminum in human colon cancer samples and its potential association with biological processes involved in cancer progression. Aluminum was found in tumor areas of 24% of patients and was associated with epithelial to mesenchymal transition (EMT) and cell death. Additional analyses revealed higher tumor mutational burden and mutations in genes related to EMT and apoptosis in aluminum-positive colon cancers. Understanding the molecular mechanisms of aluminum toxicity may improve strategies for the management of colon cancer patients.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)