Article
Ecology
Laura Martin-Torrijos, David Buckley, Ignacio Doadrio, Annie Machordom, Javier Dieguez-Uribeondo
Summary: This study assessed the genetic variation levels and patterns of freshwater crayfish populations in the Iberian Peninsula, revealing high genetic diversity significantly structured into three main genetic groups. The findings suggest the importance of considering these three phylogeographic groups as essential management units for the conservation of the species' remaining genetic diversity.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biodiversity Conservation
Leona Lovrencic, Martina Temunovic, Lena Bonassin, Frederic Grandjean, Christopher M. Austin, Ivana Maguire
Summary: The stone crayfish Austropotamobius torrentium is globally endangered due to anthropogenic pressure, climate change, and the invasive signal crayfish Pacifastacus leniusculus. The study shows that climate change is likely to result in significant loss of suitable habitats for A. torrentium, putting highly diverse populations at risk of extinction. Furthermore, the threat from climate change appears to be greater for A. torrentium than the invasive crayfish species.
GLOBAL ECOLOGY AND CONSERVATION
(2022)
Article
Fisheries
Marius-Ioan Groza, Diana Cupsa, Leona Lovrencic, Ivana Maguire
Summary: The study reported a stone crayfish population in a stream in southern lowlands of Romania, belonging to the most widespread phylogroup and sharing the same haplotype with specimens from Croatia. Unfortunately, this population likely disappeared due to crayfish plague, highlighting the vulnerability of isolated relic populations.
KNOWLEDGE AND MANAGEMENT OF AQUATIC ECOSYSTEMS
(2021)
Review
Environmental Sciences
Paula Suarez-Bregua, Miguel Alvarez-Gonzalez, Kim M. Parsons, Josep Rotllant, Graham J. Pierce, Camilo Saavedra
Summary: Monitoring marine mammal populations is crucial for assessing their status. Traditional methods have limitations, while environmental DNA (eDNA) offers a cost-effective and sensitive tool to monitor marine mammals, especially for rare, elusive, or threatened species.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Multidisciplinary Sciences
Pierfrancesco Biasetti, Linda Ferrante, Marco Bonelli, Raoul Manenti, Davide Scaccini, Barbara de Mori
Summary: This paper investigates potential ethical conflicts in the conservation of the European native crayfish Austropotamobius pallipes, emphasizing the importance of considering the principle of fairness when evaluating the economic and recreational value of invasive species. Additionally, the discussion highlights the necessity of conservation for A. pallipes due to its existence value and role as an umbrella and keystone species, offering insights for similar conservation efforts involving native species threatened by invasive competitors.
RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI
(2021)
Article
Biochemistry & Molecular Biology
Ryan B. Ghannam, Stephen M. Techtmann
Summary: Advances in nucleic acid sequencing technology have expanded our understanding of microbial diversity. Machine learning is a valuable tool for analyzing microbial community data and making predictions, but the interpretability of the models must be considered.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biodiversity Conservation
Kathrin Pascher, Vid Svara, Michael Jungmeier
Summary: Novel methods for species detection based on collection of environmental DNA have great potential in biodiversity assessment and conservation practice, offering precise and rapid species identification. These methods could serve as supplement or even substitutes for conventional monitoring methods used in protected areas.
Article
Multidisciplinary Sciences
Michael C. Allen, Robert Kwait, Anthony Vastano, Alex Kisurin, Isabelle Zoccolo, Benjamin D. Jaffe, Jordan C. Angle, Brooke Maslo, Julie L. Lockwood
Summary: This study assessed the performance of two strictly terrestrial eDNA sampling approaches to detect arboreal mammals and compared the performance of two detection methods within a single species. The results suggest that sampling eDNA from on and around trees could serve as a useful new monitoring tool for cryptic arboreal mammal communities globally.
SCIENTIFIC REPORTS
(2023)
Article
Biodiversity Conservation
Anita Tarandek, Leona Lovrencic, Lana Zidak, Martina Topic, Dorotea Grbin, Marija Gregov, Josip Curko, Sandra Hudina, Ivana Maguire
Summary: This study aims to assess how habitat alteration and subsequent water quality changes affect the stone crayfish population in the Kustosak Stream (Croatia) through three selected sites under different levels of anthropogenic disturbance. The results showed that habitat alteration caused an overall reduction in population abundance and changes in size structure, however, it had not yet resulted in detectable genetic differences. Crayfish abundance was affected by the physicochemical parameters of water, including oxygen, calcium ions, nitrates, pH, and water temperature.
Article
Food Science & Technology
Yuzhao Ling, Hongyuan Tan, Lingwei Shen, Lingyun Wei, Guangquan Xiong, Lan Wang, Wenjin Wu, Yu Qiao
Summary: The effects of ozone water and ultrasound cleaning on the microbial community diversity of crayfish were studied through microbial viable count and 16S rRNA gene sequencing. The results showed that the combined treatment significantly reduced the viable count of various microorganisms. Sensory evaluation indicated that the crayfish treated with ozone water and ultrasound cleaning provided a satisfactory sensory experience.
Article
Ecology
Elena Tricarico, Paola Ciampelli, Laura De Cicco, Sandro Aurelio Marsella, Lorenzo Petralia, Barbara Rossi, Antonio Zoccola, Giuseppe Mazza
Summary: The study shows that the presence of raccoons has negatively impacted the native crayfish populations, leading to a significant decrease or disappearance of crayfish in certain areas. Signs of raccoon presence were clearly observed, while crayfish populations remained abundant or even increased in areas where raccoons were absent. Urgent actions are needed to control raccoons and ensure the survival of the protected species.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Ecology
Maura Palacios Mejia, Connie A. Rojas, Emily Curd, Mark A. Renshaw, Kiumars Edalati, Beverly Shih, Nitin Vincent, Meixi Lin, Peggy H. Nguyen, Robert Wayne, Kelsey Jessup, Sophie S. Parker
Summary: This study investigates the impact of long-term contamination on the soil microbiome composition and diversity at an urban brownfield in Los Angeles. The findings suggest that the presence of heavy metals and organic pollutants shape the soil microbiome diversity, and certain bacteria and fungi show tolerance to these contaminants. The study recommends incorporating DNA-based multi-marker microbial community profiling in brownfield site assessment and restoration.
Article
Agronomy
Andjin Siegenthaler, Andrew K. Skidmore, G. Arjen de Groot, Ivo Laros, Melody Rousseau, Yiwei Duan
Summary: This study reveals sphere-specific microbial communities in European temperate forests, characterized by low connectivity. It emphasizes the stronger influence of microbial spheres rather than host identity. Only a few taxa inhabit both the top-canopy and soil spheres, yet they make up the majority of the abundance in each sphere.
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
Biochemistry & Molecular Biology
Opale Coutant, Cecile Richard-Hansen, Benoit de Thoisy, Jean-Baptiste Decotte, Alice Valentini, Tony Dejean, Regis Vigouroux, Jerome Murienne, Sebastien Brosse
Summary: The study found that aquatic eDNA metabarcoding has the potential to inventory mammals in Neotropical environments, providing additional data for diurnal nonaquatic species and detecting species not found in line transect surveys, such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although further developments are needed, eDNA can be used as a complement to traditional surveys.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biology
Damiano Rizzotti, Chiara Manfrin, Marco Gerdol, Samuele Greco, Gianfranco Santovito, Piero G. Giulianini
Summary: This study investigated the effect of a slight temperature rise on the erythrocyte morphology of Antarctic fish. The results showed significant temporal differences in erythrocyte shape descriptors, but no significant differences between the two experimental conditions. The study highlights the challenges of comparative physiology in studying extremely sensitive organisms and suggests that the stabling effect in aquarium facilities can obscure the effects of experimental heat treatment.
JOURNAL OF THERMAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Stefano Fornasaro, Alessandro Esposito, Fiorella Florian, Alberto Pallavicini, Luigina De Leo, Tarcisio Not, Cristina Lagatolla, Marica Mezzarobba, Alessia Di Silvestre, Valter Sergo, Alois Bonifacio
Summary: Significant differences were found in the faecal samples of celiac patients and those on a gluten-free diet using SERS spectroscopy and 16S rRNA sequencing analysis. Although there were no significant differences in bacterial composition, the relative intensity of xanthine and hypoxanthine in the SERS spectra of patients on a gluten-free diet was significantly increased.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Fisheries
Raquel Rios-Castro, Raquel Aranguren, Alejandro Romero, Elisa Banchi, Alberto Pallavicini, Beatriz Novoa, Antonio Figueras
Summary: In this study, the spatial and temporal distribution of Perkinsus olseni, a protozoan parasite, was analyzed using sequencing and real-time PCR methods. The pathogen was found to be present in water and sediment samples, showing seasonal prevalence. It was also detected in clams and for the first time in Cerastoderma edule with low abundance and infection intensity levels.
Article
Biodiversity Conservation
Chiara Manfrin, Luca Mirimin, Massimo Zanetti, Elisabetta Pizzul, Piero G. Giulianini, Alberto Pallavicini
Summary: This study developed and validated a new species-specific assay based on hydrolysis probe chemistry to detect P. parva environmental DNA (eDNA) in water samples collected in northern Italy. The results from both qPCR and qdPCR techniques showed similar findings, indicating the potential of the newly developed eDNA approach for monitoring topmouth gudgeon in freshwater ecosystems.
BIOLOGICAL INVASIONS
(2022)
Article
Biotechnology & Applied Microbiology
Federica Salatiello, Marco Gerdol, Alberto Pallavicini, Annamaria Locascio, Maria Sirakov
Summary: This study investigated the transcriptome of the bivalve mollusk Mytilus galloprovincialis to identify suitable reference genes for gene expression analyses. Through genome-wide bioinformatics analysis, the Act/Cyp-A gene pair was identified as the most appropriate for gene expression analysis across different tissues.
Article
Genetics & Heredity
Zoya Harbuzov, Valeria Farberova, Moshe Tom, Alberto Pallavicini, David Stankovic, Tamar Lotan, Hadas Lubinevsky
Summary: The present study aims to implement the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, demonstrating the high uniqueness of ASVs. By clustering and BLASTN annotation, a high-quality ASV metabarcoding reference library was selected. This library can be used to create sample ASV profiles and perform clustering.
Article
Microbiology
Timotej Turk Dermastia, Ivano Vascotto, Janja France, David Stankovic, Patricija Mozetic
Summary: Diatoms are important phytoplankton in the oceans, contributing up to 40% of photosynthetic activity and playing a vital role in carbon and silicon cycles. Traditional microscopy methods for assessing diatom diversity are unreliable, but next-generation sequencing using rbcL marker can provide more accurate results. Through comparing microscopy, 18S-V9 metabarcoding, and rbcL metabarcoding, we identified new genera and species in the Gulf of Trieste and highlighted the limitations of microscopy and reference databases.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Nicolo Gualandi, Davide Fracarossi, Damiano Riommi, Marco Sollitto, Samuele Greco, Mario Mardirossian, Sabrina Pacor, Tiago Hori, Alberto Pallavicini, Marco Gerdol
Summary: Mussels have a highly efficient innate immune system that allows them to tolerate infections well. Antimicrobial peptides (AMPs) in mussels exhibit gene presence/absence variation (PAV), resulting in a unique repertoire of defense molecules for each individual. The CRP-I gene cluster in the blue mussel was characterized, revealing the presence of numerous paralogous genes and pseudogenes. These CRP-I peptides are unlikely to function as antimicrobial agents or protease inhibitors, but they may play a role in defense against eukaryotic parasites.
Article
Biodiversity Conservation
Annalisa Scapolatiello, Chiara Manfrin, Samuele Greco, Tomislav Roncevic, Alberto Pallavicini, Sanja Puljas, Marco Gerdol
Summary: The cave systems of the Neretva River basin in the Dinaric Karst are home to the endangered stygobiotic bivalve mollusk Congeria kusceri, which is facing rapid decline due to habitat degradation and lack of effective conservation regulations. The alteration of seasonal changes in water temperatures and alkalinity is likely involved in its disappearance, as it affects shell growth, spawning, and gametogenic cycles. RNA sequencing reveals tissue-specific gene expression and a shift in energy allocation towards reproductive organs during early autumn.
Article
Biodiversity Conservation
Chiara Manfrin, Saul Ciriaco, Marco Segarich, Andrea Aiello, Fiorella Florian, Massimo Avian, Antonio Terlizzi, Piero G. Giulianini, Maurizio Spoto, Alberto Pallavicini
Summary: A species-specific assay based on hydrolysis probe chemistry was developed to detect Haplosporidium pinnae DNA in feces and pseudofeces of Pinna nobilis. The assay successfully detected H. pinnae in the feces of fan mussels in spring but not during summer. This noninvasive method can be used to monitor early-stage H. pinnae infections and routinely screen for the pathogen in live fan mussels and other environmental matrices.
Article
Fisheries
Samuele Greco, Giacomo Voltarel, Anastasia Serena Gaetano, Chiara Manfrin, Alberto Pallavicini, Piero Giulio Giulianini, Marco Gerdol
Summary: Antarctica is an extreme continent with freezing temperatures and harsh conditions, but the Antarctic Ocean is surprisingly diverse in terms of living organisms. This study focuses on the Antarctic scallop Adamussium colbecki and investigates its molecular adaptations to survive in freezing waters. The analysis reveals over-expression of genes involved in mRNA regulation, protein degradation, and cytoskeletal maintenance, shedding light on the adaptive traits of this species.
Article
Fisheries
Samuele Greco, Anastasia Serena Gaetano, Gael Furlanis, Francesca Capanni, Chiara Manfrin, Piero Giulio Giulianini, Gianfranco Santovito, Paolo Edomi, Alberto Pallavicini, Marco Gerdol
Summary: The Antarctic continent, though pristine, is highly vulnerable to climate change. This study focused on investigating the effects of a moderate increase in temperature on the emerald rockcod, Trematomus bernacchii, and identified the brain as the most susceptible tissue to heat stress.
Meeting Abstract
Immunology
A. Scapolatiello, U. Rosani, C. Manfrin, S. Puljas, A. Pallavicini, M. Gerdol
ISJ-INVERTEBRATE SURVIVAL JOURNAL
(2022)
