Marine invasive alien species in Europe: 9 years after the IAS Regulation

Biological invasions, resulting from human activities, exert substantial impacts on ecosystems worldwide. This review focuses on marine invasive alien species (IAS) in Europe, examining the current state, proposing strategies to address the problem, and offering recommendations for enhanced management. Effective management of biological invasions relies on accessible, accurate data to inform decision-making. Information systems such as the European Alien Species Information Network (EASIN), Aquatic Non-Indigenous and Cryptogenic Species (AquaNIS), and World Register of Introduced Marine Species (WriMS) provide comprehensive databases on IAS, but their sustainability requires long-term maintenance, continuous updates, and support. Most countries lack specific monitoring programs for marine IAS, and standardization and improvement of monitoring methods are needed. Port monitoring plays a vital role in the early detection of new arrivals, and recent advancements in molecular techniques show promise for effective IAS monitoring. Risk screening tools are commonly employed to rank taxa based on their invasiveness potential in European regions, but variations in protocols can yield inconsistent results. European impact assessments highlight resource competition, novel habitat creation, and predation as primary mechanisms for negative impacts on biodiversity, while the creation of novel habitats represents a key mechanism for positive impacts. Preventing IAS introductions is critical, and measures such as ballast water treatment systems are implemented to reduce the likelihood of marine introductions. However, understanding introduction pathways remains uncertain for many IAS. Eradication and control efforts for marine IAS have limited success, emphasizing the need for enhanced biosecurity measures. Climate change, especially ocean warming, can intensify IAS impacts on native species and ecosystems. In climate change hotspots, some tropical aliens may, however, compensate for the loss of thermally sensitive natives with similar traits. Therefore, it is imperative to consider the interactions between climate change and IAS in developing effective management and conservation strategies. Enhancing IAS management in Europe entails i) securing adequate funding, ii) expanding the list of IAS of Union Concern to adequately cover marine invasions, iii) learning from countries with successful biosecurity practices, iv) sustaining information systems, v) improving monitoring and early warning systems with innovative technologies, vi) enhancing prediction models, vii) conducting integrated impact assessments and mapping cumulative IAS impacts, and vii) considering the potential benefits of IAS in ecosystem functioning and services

3 year report on activities for the Working Group on Phytoplankton and Microbial Ecology (WGPME)

The ICES Working Group on Phytoplankton and Microbial Ecology (WGPME) provides tools and expert perspectives on the sampling methods, ecology and diversity of phytoplankton and other planktonic microbes. The group set out terms of reference to improve access to data, crossdisciplinary approaches and to develop ecological interpretations of the changing phytoplankton seascape. The group published 16 papers between 2019–2021, including key tools, high-profile synthesis papers and science reports. Tools: The group has progressed efforts to collect images of commonly used Lugol’s-preserved phytoplankton, alongside live images to aid those in correctly identifying species. Members have noticed and published records of new phytoplankton species. The group aims to produce a New Records database to assist in notifying new or reoccurrence of a species. WGPME work, with other Expert Groups (EG) to improve access to molecular genetic tools and records. A multi-EG thematic session has been submitted for ICES ASC 2022 in cooperation with other EGs, whilst phytoplankton barcoding information will be incorporated into the Working Group on Integrated Morphological and Molecular Taxonomy (WGIMT) barcoding Atlas (https://metazoogene.org/atlas). Information and access: The group is gathering information on nano and picoplankton (small phytoplankton less than 10 and 2µm respectively) to incorporate into global datasets such as GLOMICON. Multiple data sources point to an increasing trend in picoplankton and few indicators exist in current EU or national legislation to measure their impact on marine ecology. Many members are involved in indicator development for governmental and pan-governmental organisations such as OSPAR. However, the number and level of indicators vary in each country. Long-term ecology: The cooperative zooplankton and phytoplankton report has been delayed but initial analysis has indicated ≥30 years of data reliably shows spatio-temporal trends in phytoplankton and the effects of temperature on key phytoplankton groups. Two research papers are being produced on climate change effects on key marine phytoplankton species with the additional aim of improving indicators of change using species-specific information

Next-Generation Global Biomonitoring: Large-scale, Automated Reconstruction of Ecological Networks

We foresee a new global-scale, ecological approach to biomonitoring emerging within the next decade that can detect ecosystem change accurately, cheaply, and generically. Next-generation sequencing of DNA sampled from the Earth's environments would provide data for the relative abundance of operational taxonomic units or ecological functions. Machine-learning methods would then be used to reconstruct the ecological networks of interactions implicit in the raw NGS data. Ultimately, we envision the development of autonomous samplers that would sample nucleic acids and upload NGS sequence data to the cloud for network reconstruction. Large numbers of these samplers, in a global array, would allow sensitive automated biomonitoring of the Earth's major ecosystems at high spatial and temporal resolution, revolutionising our understanding of ecosystem change

Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches

The incursion of High-Throughput Sequencing (HTS) in environmental microbiology brings unique opportunities and challenges. HTS now allows a high-resolution exploration of the vast taxonomic and metabolic diversity present in the microbial world, which can provide an exceptional insight on global ecosystem functioning, ecological processes and evolution. This exploration has also economic potential, as we will have access to the evolutionary innovation present in microbial metabolisms, which could be used for biotechnological development. HTS is also challenging the research community, and the current bottleneck is present in the data analysis side. At the moment, researchers are in a sequence data deluge, with sequencing throughput advancing faster than the computer power needed for data analysis. However, new tools and approaches are being developed constantly and the whole process could be depicted as a fast co-evolution between sequencing technology, informatics and microbiologists. In this work, we examine the most popular and recently commercialized HTS platforms as well as bioinformatics methods for data handling and analysis used in microbial metagenomics. This non-exhaustive review is intended to serve as a broad state-of-the-art guide to researchers expanding into this rapidly evolving field

Genomic Sequence and Analysis of EhV-99B1, a New Coccolithovirus from the Norwegian Fjords

Coccolithoviruses are giant dsDNA viruses that infect Emiliania huxleyi, the most ubiquitous marine microalga. Here, we present the genome of the latest coccolithovirus strain to be sequenced, EhV-99B1, and compare it with two other coccolithovirus genomes (EhV-86 and EhV-163). EhV-99B1 shares a pairwise nucleotide identity of 98% with EhV-163 (the two strains were isolated from the same Norwegian fjord but in different years), and just 96.5% with EhV-86 (isolated in the same spring as EhV-99B1 but in the English Channel). We confirmed and extended the list of relevant genomic differences between these EhVs from the Norwegian fjord and EhVs from the English Channel, namely the removal/insertions of: a phosphate permease, an endonuclease, a transposase, and two specific tRNAs. As a whole, this study provided new clues and insights into the diversity and mechanisms driving the evolution of these large oceanic viruses, in particular those processes involving selfish genetic elements

CREST - Classification Resources for Environmental Sequence Tags

10.1371/journal.pone.0049334PLoS ONE711e4933

The impact of DNA extract homogenization and replication on marine sediment metabarcoding diversity and heterogeneity

Metabarcoding of environmental DNA (eDNA) is an attractive complement to morphological methods for surveys and routine monitoring of marine sediment benthic communities. However, metabarcoding and other genetic techniques are heavily affected by choices made during sampling, processing, and analysis. Here, we investigated the effect of different eDNA extraction protocols on observed alpha- and beta diversity of replicates from the same grab. Specifically, we compared (A) homogenization intensity during sediment DNA extraction, (B) extraction replicates vs larger sediment extraction volume, and (C) pre- and post-PCR extract pooling. Using the 18S V1-V2 region marker, we show that a Precellys homogenizer protocol during DNA extraction can significantly improve sediment metabarcoding results in terms of captured diversity and inter-replicate homogeneity compared to vortexing only. This effect superseded that of increased sediment extract volume. Pre-PCR pooling of DNA extraction replicates increased observed rarefied richness compared to data from single extracts only, but not to the extent of sample extract replicates amplified individually before pooling. We argue that this discrepancy was due to a reduction both in recovered sample diversity, but also the number of PCR artifacts and PCR drift. Our results demonstrate that extraction replicates of smaller sediment volumes, in combination with moderate Precellys homogenization and pre-PCR pooling, are a cost-effective way to increase the amount of organism diversity that is recovered from sediment eDNA metabarcoding samples