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
Rosetta C. Blackman, Jeanine Brantschen, Jean-Claude Walser, Remo Wuethrich, Florian Altermatt
Summary: Regular monitoring of ecosystems is important for the early detection and management of invasive alien species (IAS). Current monitoring methods for freshwater IAS can be costly and time-consuming. This study compares the effectiveness of environmental DNA (eDNA) metabarcoding and traditional kick-net sampling for monitoring freshwater macroinvertebrate IAS. Both methods have their strengths, with kick-net sampling being more successful for detecting well-known target IAS, while eDNA samples are complementary for detecting unnoticed IAS. The study shows that eDNA is easily implemented in national- and catchment-scale monitoring, but success is dependent on primer choice, species biology, and available markers.
RIVER RESEARCH AND APPLICATIONS
(2022)
Article
Ecology
Michael Tessler, Seth W. W. Cunningham, Melissa R. R. Ingala, Sally D. D. Warring, Mercer R. R. Brugler
Summary: Environmental DNA (eDNA) sequencing, which collects DNA from living cells or shed DNA in the environment, has greatly benefited microbial ecologists. With the advancement of metabarcoding and metagenomics, eDNA methods have become increasingly powerful and affordable. However, these methods are evolving rapidly, making it overwhelming for newcomers. This review provides a starting point for microbial ecologists, covering study design, sample collection, sequencing technology selection, lab protocols, equipment, and bioinformatic tools, with a focus on the application of eDNA in restoration.
Article
Biodiversity Conservation
Cecilia Villacorta-Rath, Lori Lach, Natalia Andrade-Rodriguez, Damien Burrows, Dianne Gleeson, Alejandro Trujillo-Gonzalez
Summary: Terrestrial invasive invertebrates can be detected using targeted environmental DNA (eDNA) methods, which can transport eDNA from land into adjacent waterbodies. In this study, eDNA from the invasive yellow crazy ant was successfully isolated and amplified from water samples collected near infestations, even from sites located 300 m away. Our findings demonstrate the potential of eDNA as a useful tool for detecting terrestrial invertebrates.
Review
Biodiversity Conservation
Vera G. G. Fonseca, Phil I. I. Davison, Veronique Creach, David Stone, David Bass, Hannah J. J. Tidbury
Summary: Aquatic non-indigenous species (NIS) pose threats to biodiversity, ecosystem functions, and the global economy. Traditional methods of NIS monitoring have limitations, leading to the development of DNA-based methods, particularly environmental DNA (eDNA) tools, which offer rapid and cost-effective detection of NIS. eDNA tools can increase detection and sensitivity for rare and elusive species, making them valuable as early warning tools. Balancing method sensitivity, logistical requirements, and costs is crucial for future management decisions.
Article
Biochemistry & Molecular Biology
Kaushar Kagzi, Robert M. Hechler, Gregor F. Fussmann, Melania E. Cristescu
Summary: This study investigates the degradation of environmental DNA (eDNA) and environmental RNA (eRNA) under different pH conditions. The results show that eRNA decays more rapidly than eDNA, and eDNA degrades more slowly under acidic conditions. This study provides a basis for assessing the persistence and degradation dynamics of eRNA and eDNA under ecologically relevant pH conditions.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Kara J. Andres, David M. Lodge, Jose Andres
Summary: Environmental DNA (eDNA) sampling is a powerful and efficient approach for collecting information about species, and it may also provide information about population-level genetic variability. In this study, the researchers used eDNA sampling to estimate the genetic diversity and structure of an invasive fish species in the Great Lakes region. The study found that the genetic patterns observed from eDNA analysis were consistent with conventional tissue-based estimates. This research highlights the potential for eDNA sampling to reveal detailed population characteristics that can inform monitoring and management plans for difficult-to-sample species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Rachel M. Fricke, Julian D. Olden
Summary: This article provides a synthetic perspective on innovative technologies for invasive species management, including pathway intervention, spread prevention, impact mitigation, and public engagement. It also introduces tools that facilitate big data processing, such as automated image and text recognition based on machine learning. Finally, it explores the challenges and opportunities for integrating emerging technologies into invasive species management.
Review
Biodiversity Conservation
Kailash Bohara, Amit K. Yadav, Pabitra Joshi
Summary: Organisms release their nucleic acid into the environment, and eDNA/eRNA techniques are used to detect them. These techniques are being extensively employed in aquaculture and fisheries settings to identify different organisms and pathogens. However, the reliability of results can be challenging due to nucleic acid degradation. This review discusses the detection of aquaculture diseases and parasites using eDNA/eRNA methods and the fate of nucleic acids in different water quality and environmental parameters.
Article
Ecology
Nicholas J. Foster, Richard F. Maloney, Philip J. Seddon, Mariano Rodriguez-Recio, Yolanda van Heezik
Summary: This study aims to assess whether high-elevation landforms can limit the movements of invasive small mammals and improve the success of eradication programs. Based on species' distributions and spatial predictions, the researchers identified landforms that can act as dispersal barriers. The findings suggest that high-elevation landforms have the potential to significantly enhance the effectiveness of eradication programs by restricting the movement of target species.
Article
Biochemistry & Molecular Biology
Bastian Egeter, Joana Verissimo, Manuel Lopes-Lima, Catia Chaves, Joana Pinto, Nicoletta Riccardi, Pedro Beja, Nuno A. Fonseca
Summary: This study provides a laboratory protocol and bioinformatic tools for detecting aquatic invasive species using nanopore sequencing technology, and compares it with Illumina-based sequencing. Testing was conducted at sampling sites in Italy and Portugal, showing a high degree of agreement between the two sequencing methods and faster sample processing time for nanopore sequencing.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Ecology
Ilze Pretorius, Wayne C. Schou, Brian Richardson, Shane D. Ross, Toni M. Withers, David G. Schmale III, Tara M. Strand
Summary: Invasive species, which are carried by wind, pose unquantified and difficult-to-manage biosecurity threats to human, animal, and plant health in various ecosystems. The lack of tools to predict these invasion events reflects their complexity. This study provides evidence that the long-distance aerial dispersal of invasive insects and wildfire smoke, a potential carrier of invasive species, is driven by atmospheric pathways known as Lagrangian coherent structures (LCS). A modeling system combining LCS modeling with species biology and atmospheric survival has the potential to greatly improve the understanding and prediction of atmospheric invasions.
ECOLOGICAL APPLICATIONS
(2023)
Article
Biology
Susana Carvalho, Hailey Shchepanik, Eva Aylagas, Michael L. Berumen, Filipe O. Costa, Mark John Costello, Sofia Duarte, Jasmine Ferrario, Oliver Floerl, Moritz Heinle, Stelios Katsanevakis, Agnese Marchini, Sergej Olenin, John K. Pearman, Raquel S. Peixoto, Lotfi J. Rabaoui, Greg Ruiz, Greta Srebaliene, Thomas W. Therriault, Pedro E. Vieira, Anastasija Zaiko
Summary: Managing marine nonindigenous species is challenging due to the highly connected marine environments that allow for the dispersal of species across geopolitical borders. Inconsistent biosecurity management across borders can lead to the spread of nonindigenous species, often unnoticed or unreported. Collaborative surveillance programs and databases can enhance early detection and information exchange, while local reference libraries, databases, and predictive modeling can aid in biosecurity program development.
Article
Environmental Sciences
Iveta Matejusova, Jennifer Graham, Fiona Bland, Jean-Pierre Lacaze, Guillaume Herman, Lyndsay Brown, Eric Dalgarno, John D. Bishop, Jenni E. Kakkonen, Kirsty F. Smith, Alex Douglas
Summary: The study presents a qPCR assay for detecting the invasive tunicate D. vexillum with high sensitivity, utilizing eDNA in water samples. Water sample analyses showed variation in detection consistency within infected sites, with sites of lower consistency typically having low D. vexillum density or undergoing management efforts.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Environmental Studies
Flavius Balacenoiu, Anze Japelj, Iris Bernardinelli, Bastien Castagneyrol, Gyorgy Csoka, Milka Glavendekic, Gernot Hoch, Boris Hrasovec, Silvija Krajter Ostoic, Marton Paulin, David Williams, Johan Witters, Maarten de Groot
Summary: Against the backdrop of globalization, invasive alien species (IAS) have caused biological invasions with negative effects on economies, human health, and the environment. Preventive actions, such as early detection and public awareness, are considered the most effective methods to control IAS. A questionnaire circulated in ten European countries was used to assess the knowledge of stakeholders in the forestry sector regarding IAS. The results showed that the majority of respondents had heard about IAS and had a correct understanding of these organisms, with stakeholders in the forestry sector being more aware of their impact.
Article
Biochemistry & Molecular Biology
Ulla von Ammon, Xavier Pochon, Paula Casanovas, Branwen Trochel, Martin Zirngibl, Austen Thomas, Jan Witting, Paul Joyce, Anastasija Zaiko
Summary: This study aimed to optimize environmental DNA (eDNA) sampling by comparing two different sampling methods and filters, and assessing their impact on biodiversity through metabarcoding analysis. The results showed that bucket sampling combined with self-preserving filters had the highest amplicon sequence variant (ASV) richness, while net sampling combined with 5μm pore size filters captured more metazoan taxa. These findings are important for optimizing eDNA sampling protocols in marine biodiversity research and surveillance.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Ecology
Oliver Dalby, Nicolas Pucino, Yi Mei Tan, Emma L. Jackson, Peter Macreadie, Rhys A. Coleman, Mary A. Young, Daniel Ierodiaconou, Craig D. H. Sherman
Summary: This article discusses the information required for seagrass restoration and how to identify target areas for restoration efforts through analysis of spatio-temporal trends. Remote sensing techniques can accurately monitor seagrass ecosystems and guide the allocation of restoration resources.
RESTORATION ECOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jean-Francois Doherty, Upendra R. Bhattarai, Sara Ferreira, Robert Poulin, Neil J. Gemmell, Eddy J. Dowle
Summary: Almost every animal trait is strongly associated with parasitic infection or potential exposure to parasites. Accurately determining the status and severity of endoparasitic infection without killing and dissecting the host is a major challenge researchers face. This study demonstrates a noninvasive and minimally stressful method for detecting endoparasitic infection with greater accuracy than dissection alone, improving protocols for live animal studies.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Gert-Jan Jeunen, Eddy Dowle, Jonika Edgecombe, Ulla von Ammon, Neil J. Gemmell, Hugh Cross
Summary: The measurement of biodiversity plays a vital role in life science research. However, the reliability and accuracy of taxonomic assignment in metabarcoding sequencing data greatly depend on the quality and completeness of reference databases. To address this issue, researchers have developed crabs, a software package that allows the creation of curated reference databases for metabarcoding studies.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Gert-Jan Jeunen, Jasmine S. Cane, Sara Ferreira, Francesca Strano, Ulla von Ammon, Hugh Cross, Robert Day, Sean Hesseltine, Kaleb Ellis, Lara Urban, Niall Pearson, Pamela Olmedo-Rojas, Anya Kardailsky, Neil J. Gemmell, Miles Lamare
Summary: Aquatic environmental DNA (eDNA) surveys are revolutionizing marine ecosystem monitoring, but the time-consuming active filtration step remains a bottleneck. This study investigated the similarities and differences between eDNA signals obtained from various sources, including water, filter-feeding organisms, and sponge material. The results showed that vertebrate eDNA signals from water and sponge samples were highly concordant, highlighting the potential of using marine sponges as an additional tool for eDNA-based biodiversity surveys. Caution should be taken to minimize the impact on marine communities during eDNA sampling.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Fisheries
S. Muncaster, A. Goikoetxea, P. M. Lokman, C. E. Moraes, E. L. Damsteegt, J. Edgecombe, N. J. Gemmell, E. V. Todd
Summary: Socially induced sex change is regulated by a combination of genes and epigenetic factors that control sex differentiation and cell fate. The molecular basis for this transformation is still largely unknown. Recent research suggests that both epigenetic effects and genes involved in cell fate are important drivers of sex change.
REVIEWS IN FISH BIOLOGY AND FISHERIES
(2023)
Article
Environmental Sciences
Henn Ojaveer, Heli Einberg, Maiju Lehtiniemi, Okko Outinen, Anastasija Zaiko, Anders Jelmert, Jonne Kotta
Summary: This study quantitatively assessed the impacts of widespread non-indigenous species (NIS) on ecosystem services (ES) in the Baltic Sea. The results showed that these NIS had significant effects on ES, particularly regulation services. This method can be applied to other ecosystems to better understand human impacts on ES.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Manfred Lenzen, Mimi Tzeng, Oliver Floerl, Anastasija Zaiko
Summary: The majority of global cargo trade is conducted by maritime shipping, which can lead to the dispersal and establishment of non-indigenous species (NIS) beyond their natural ranges. These NIS cause significant impacts on the environment, economy, culture, and human health. The authors develop a novel approach using economic analysis techniques to assess the risks of global marine NIS transfer, which can predict biosecurity risks based on trade connections and commodities. They demonstrate the usefulness of their approach with a case study tracing the spread of a hypothetical marine NIS from Japan. Their study shows that biosecurity risk can be assessed using economic modelling frameworks based on monetary transaction data alone.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biochemistry & Molecular Biology
Allison K. Miller, Cara L. Brosnahan, Anjali Pande, Cindy F. Baker, Jemma L. Geoghegan, Jane Kitson, Neil J. Gemmell, Edwina J. Dowle
Summary: Infectious diseases have a significant impact on various organisms, and understanding the interactions between hosts and pathogens is crucial for their conservation and management. The use of genomic approaches has made it easier to obtain this knowledge quickly, however, many species still face challenges in accessing appropriate samples and data. Archival materials, such as formalin-fixed paraffin-embedded tissue samples, may provide a valuable resource for studying pathogen emergence and host responses over long periods of time.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Zoology
Kaj Kamstra, Chloe van der Burg, Haylee M. Quertermous, Simon Muncaster, Erica V. Todd, Christine L. Jasoni, Culum Brown, Neil J. Gemmell
Summary: For most vertebrates, sexual fate is genetically determined and remains fixed throughout life. However, for some teleost fishes sex is more plastic. Significant progress has been made in characterising the cellular and molecular processes that underpin gonadal sex change. The brain-mediated mechanisms that underlie and initiate this transformation, however, remain poorly understood.
NEW ZEALAND JOURNAL OF ZOOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Andrew T. M. Bagshaw, Neil J. Gemmell
Summary: In recent years, scientists have shifted their focus from studying the relationships between adjacent nucleotides to exploring the larger scale structure of DNA. A little-known technique called non-denaturing bisulfite modification of genomic DNA in conjunction with high-throughput sequencing has provided valuable insights. This technique has revealed a gradient in reactivity that increases towards the 5' end of poly-dC:dG mononucleotide repeats, suggesting the presence of positive-roll bending not predicted by existing models. Furthermore, these repeats are enriched at positions relative to the nucleosome dyad that bend towards the major groove, providing important information about DNA packaging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Ecology
Yi Mei Tan, Rhys A. Coleman, Peter A. Biro, Oliver Dalby, Emma L. Jackson, Laura L. Govers, Jannes H. T. Heusinkveld, Peter I. Macreadie, Mogens R. Flindt, Jack Dewhurst, Craig D. H. Sherman
Summary: The use of seed- and shoot-based restoration approaches for Z. muelleri in Victoria, Australia was explored through field trials. Seed collections and germination achieved good results, with seed collection rates improving from 489 to 1,939 seeds/hour over 2 years and in situ seedling germination rates increasing from a maximum of 10.80% to 25.25% over 2 years. In contrast, shoot-based restoration approaches were more variable, with plants transplanted with their sediment-intact outperforming all bare-rooted approaches. Seed-based approaches have the potential to be viable and scalable for Z. muelleri, but further studies are needed to improve seedling survival and in situ germination rates.
RESTORATION ECOLOGY
(2023)
Article
Cell Biology
Nataliya Timoshevskaya, Kaan Eskut, Vladimir A. Timoshevskiy, Sofia M. C. Robb, Carson Holt, Jon E. Hess, Hugo J. Parker, Cindy F. Baker, Allison K. Miller, Cody Saraceno, Mark Yandell, Robb Krumlauf, Shawn R. Narum, Ralph T. Lampman, Neil J. Gemmell, Jacquelyn Mountcastle, Bettina Haase, Jennifer R. Balacco, Giulio Formenti, Sarah Pelan, Ying Sims, Kerstin Howe, Olivier Fedrigo, Erich D. Jarvis, Jeramiah J. Smith
Summary: Programmed DNA loss is a gene silencing mechanism found in various vertebrate and nonvertebrate lineages. The evolution of somatically eliminated sequences in these species has been difficult to reconstruct due to repetitive and duplicated sequences. However, an improved assembly of the sea lamprey genome has enabled analysis that sheds light on the recruitment of genes to the germline-specific fraction and reveals the roles of segmental duplication and positive selection in the long-term evolution of germline-specific chromosomes.
