DNA metabarcoding derived biotic indices for marine monitoring and assessment

238 p.La Directiva Marco del Agua y la Directiva Marco de la Estrategia Marina tienen como principal objetivo proteger y restaurar los ecosistemas acuáticos, para lo cual es necesario evaluar el estado ecológico de una manera que permita realizar una gestión de los ecosistemas de forma integrada. Para ello, dicha evaluación se basa en el seguimiento de una serie de indicadores. No obstante, en los últimos años ha aumentado la necesidad tanto de desarrollar nuevas técnicas de seguimiento de los indicadores como de incluir indicadores nuevos que permitan realizar una evaluación ambiental más rápida, precisa y eficaz en términos económicos. Entre las herramientas innovadoras más prometedoras que permiten facilitar el seguimiento del estado y dar lugar a nuevos indicadores se encuentran las técnicas basadas en genómica, de las cuales cabe destacar el metabarcoding. Esta técnica permite realizar de forma simultánea la identificación taxonómica en numerosas muestras ambientales, de manera precisa y a bajo coste, lo que facilita la caracterización de comunidades biológicas, incluyendo cualquier estado de desarrollo, especies crípticas e incluso especímenes degradados. No obstante, antes de incluir el metabarcoding como herramienta de evaluación ambiental en directivas europeas, es necesario comparar su capacidad para generar los mismos resultados que los obtenidos con las herramientas tradicionales para la identificación de especies (basadas en caracteres morfológicos) y, por tanto, examinar su potencial para incluir nuevos indicadores de evaluación del estado. Esta Tesis investiga la aplicación del metabarcoding para responder a la necesidad de desarrollar nuevas herramientas de seguimiento que disminuyan costes y permitan llevar a cabo una evaluación ambiental integrada.Azti Teknalia (Fundación Centros Tecnológicos). DEVOTES (Development Of Innovative Tools for understanding marine biodiversity and assessing good Environmental Status). URA . Ur agentzia. Eusko Jaurlaritza-Gobierno Vasc

Evaluación de la toxicidad de fitoplancton marino mediante la aplicación de bioensayos con invertebrados marinos

The dinoflagellate Alexandrium minutum and the haptophyte Prymnesium parvum are well known for their toxin production and negative effects in marine coastal environments. A. minutum produces toxins which cause paralytic shellfish poisoning in humans and can affect copepods, shellfish and other marine organisms. Toxins of P. parvum are associated with massive fish mortalities resulting in negative impacts on the marine ecosystem and large economic losses in commercial aquaculture. The aim of this work is to improve our knowledge about the reliability of the use of marine invertebrate bioassays to detect microalgae toxicity, by performing: (i) a 24- to 48-h test with the brine shrimp Artemia franciscana; (ii) a 48-hour embryo-larval toxicity test with the sea urchin Paracentrotus lividus; and (iii) a 72-h test with the amphipod Corophium multisetosum. The results indicate that A. franciscana and P. lividus larvae are sensitive to the toxicity of A. minutum and P. parvum. LC50 comparison analysis between the tested organisms reveals that A. franciscana is the most sensitive organism for A. minutum. These findings suggest that the use of different organizational biological level bioassays appears to be a suitable tool for A. minutum and P. parvum toxicity assessment.Las microalgas Alexandrium minutum y Prymnesium parvum son bien conocidas por la producción de toxinas y sus efectos negativos en nuestras costas. A. minutum produce la toxina PSP (Paralytic Shellfish Poisoning) que afecta a humanos y una gran variedad de organismos marinos como copépodos y marisco. Las toxinas de P. parvum producen grandes mortalidades de peces ocasionando graves impactos negativos en el ecosistema marino e importantes pérdidas económicas en acuicultura. Este trabajo tiene como objetivo mejorar el conocimiento del uso de bioensayos con invertebrados marinos en la detección de la toxicidad de microalgas, mediante: (i) un test de 24-48 horas con Artemia franciscana; (ii) un test de 48 horas con embriones y larvas del erizo de mar Paracentrotus lividus; y (iii) un test de 72 horas con el anfípodo Corophium multisetosum. Los resultados muestran que las larvas de A. franciscana y P. lividus son sensibles a la toxicidad de A. minutum y P. parvum. Los análisis LC50 revelan que A. franciscana es el organismo más sensible a A. minutum. Estos resultados indican que los bioensayos con diferentes niveles de organización biológica parecen ser una herramienta apropiada para la evaluación de la toxicidad de A. minutum y P. parvum

A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring

Environmental genomics is a promising field for monitoring biodiversity in a timely fashion. Efforts have increasingly been dedicated to the use of bacteria DNA derived data to develop biotic indices for benthic monitoring. However, a substantial debate exists about whether bacteria‐derived data using DNA metabarcoding should follow, for example, a taxonomy‐based or a taxonomy‐free approach to marine bioassessments. Here, we showcase the value of DNA‐based monitoring using the impact of fish farming as an example of anthropogenic disturbances in coastal areas and compare the performance of taxonomy‐based and taxonomy‐free approaches in detecting environmental alterations. We analysed samples collected near to the farm cages and along distance gradients from two aquaculture installations, and at control sites, to evaluate the effect of this activity on bacterial assemblages. Using the putative response of bacterial taxa to stress we calculated the taxonomy‐based biotic index microgAMBI. The distribution of individual amplicon sequence variants (ASVs), as a function of a gradient in sediment acid volatile sulphides, was then used to derive a taxonomy‐free bacterial biotic index specific for this data set using a de novo approach based on quantile regression splines. Our results show that microgAMBI revealed a organically enriched environment along the gradient. However, the de novo biotic index outperformed microgAMBI by providing a higher discriminatory power in detecting changes in abiotic factors directly related to fish production, whilst allowing the identification of new ASVs bioindicators. The de novo strategy applied here represents a robust method to define new bioindicators in regions or habitats where no previous information about the response of bacteria to environmental stressors exists.This work was partially funded by the project CGL2015-70136-R from the Spanish Ministry of Economy and Competitiveness (MINECO) and the EU ERDF funding program. E.A. and S.C. are supported by funding from a collaboration between KAUST and Saudi Aramco within the framework of the Saudi Aramco –KAUST Center for Marine Environmental Observations. K.T.-G. is supported by Ministerio de Ciencia, Innnovación y Universidades through the Juan de la Cierva Incorporación program (IJCI-2017-34174)

The Right Place at the Right Time: Seasonal Variation of Bacterial Communities in Arid Avicennia marina Soils in the Red Sea Is Specific to Its Position in the Intertidal

Mangrove forests play an important role in facilitating biogeochemical pathways and cycling acting as blue carbon sinks. These services are primarily regulated by the activity of the soil microbiome. However, there is still limited research into spatial and temporal variation patterns of bacterial community assemblages in mangrove soils. This study investigated important ecological scales of microprocesses that govern microbial communities in an arid mangrove ecosystem. Shifts in microbial community composition were influenced by fluctuations in environmental factors within the mangrove forests of the Red Sea influenced by seasonal changes in sea level. Notably, in summer microbial communities in shrub sites differed significantly from the fringe and the winter samples, with lower alpha diversity yet a higher dominance of specialized species capable of surviving in extreme conditions. The onset of dispersal limitation and heterogenous selection and the reduction of drift are likely the main forces shaping community assemblages. Specifically, in summer lower mean tidal levels eliminate tidal inundation creating a harsh high salinity and high temperature environment with no tidal connection thereby influencing the onset of dispersal limitation. An increased understanding of the spatial and temporal variation of bacterial communities is critical when assessing delivery of ecosystem services and their role in soil biogeochemical processes

Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or “in development”, hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.publishedVersio

Hurdles and opportunities in implementing marine biosecurity systems in data-poor regions

Managing marine nonindigenous species (mNIS) is challenging, because marine environments are highly connected, allowing the dispersal of species across large spatial scales, including geopolitical borders. Cross-border inconsistencies in biosecurity management can promote the spread of mNIS across geopolitical borders, and incursions often go unnoticed or unreported. Collaborative surveillance programs can enhance the early detection of mNIS, when response may still be possible, and can foster capacity building around a common threat. Regional or international databases curated for mNIS can inform local monitoring programs and can foster real-time information exchange on mNIS of concern. When combined, local species reference libraries, publicly available mNIS databases, and predictive modeling can facilitate the development of biosecurity programs in regions lacking baseline data. Biosecurity programs should be practical, feasible, cost-effective, mainly focused on prevention and early detection, and be built on the collaboration and coordination of government, nongovernment organizations, stakeholders, and local citizens for a rapid response.This work resulted from a workshop organized at the King Abdul- lah University of Science and Technology and sponsored under the Support for Conferences and Workshops Program. We would like to thank the admin support of the Red Sea Research Cen- ter team, IT, and teachers and students from the KAUST schools who participated in some outreach activities. We thank Ana Bi- gio for the artwork presented in this article (figures 1–4). GS was supported by the European Social Fund, under project no 09.3.3- LMT-K-712, the “Development of Competences of Scientists, other Researchers and Students through Practical Research Activities” measure, grant agreement no. 09.3.3-LMT-K-712–19-0083

A Synthesis of Marine Monitoring Methods With the Potential to Enhance the Status Assessment of the Baltic Sea

Highlights - We rated novel methods regarding their ability to improve the Baltic Sea monitoring. - Methods were assessed with respect to their costs and applicability. - All methods can potentially increase data resolution or monitor novel ecosystem elements. - We recommend several novel methods for the Baltic status assessment.A multitude of anthropogenic pressures deteriorate the Baltic Sea, resulting in the need to protect and restore its marine ecosystem. For an efficient conservation, comprehensive monitoring and assessment of all ecosystem elements is of fundamental importance. The Baltic Marine Environment Protection Commission HELCOM coordinates conservation measures regulated by several European directives. However, this holistic assessment is hindered by gaps within the current monitoring schemes. Here, twenty-two novel methods with the potential to fill some of these gaps and improve the monitoring of the Baltic marine environment are examined. We asked key stakeholders to point out methods likely to improve current Baltic Sea monitoring. We then described these methods in a comparable way and evaluated them based on their costs and applicability potential (i.e., possibility to make them operational). Twelve methods require low to very low costs, while five require moderate and two high costs. Seventeen methods were rated with a high to very high applicability, whereas four methods had moderate and one low applicability for Baltic Sea monitoring. Methods with both low costs and a high applicability include the Manta Trawl, Rocket Sediment Corer, Argo Float, Artificial Substrates, Citizen Observation, Earth Observation, the HydroFIA®pH system, DNA Metabarcoding and Stable Isotope Analysis

Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.info:eu-repo/semantics/publishedVersio

Environmental status assessment using DNA metabarcoding: towards a genetics based Marine Biotic Index (gAMBI).

Marine ecosystem protection and conservation initiatives rely on the assessment of ecological integrity and health status of marine environments. The AZTI's Marine Biotic Index (AMBI), which consists on using macroinvertebrate diversity as indicator of ecosystem health, is used worldwide for this purpose. Yet, this index requires taxonomic assignment of specimens, which typically involves a time and resource consuming visual identification of each sample. DNA barcoding or metabarcoding are potential harmonized, faster and cheaper alternatives for species identification, although the suitability of these methods for easing the implementation of the AMBI is yet to be evaluated. Here, we analyze the requirements for the implementation of a genetics based AMBI (gAMBI), and show, using available sequence data, that information about presence/absence of the most frequently occurring species provides accurate AMBI values. Our results set the basics for the implementation of the gAMBI, which has direct implications for a faster and cheaper marine monitoring and health status assessment