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1.
Nucleic Acids Res ; 51(W1): W438-W442, 2023 07 05.
Artículo en Inglés | MEDLINE | ID: mdl-37207328

RESUMEN

Advances in high-throughput sequencing (HTS) technologies and their increasing affordability have fueled environmental DNA (eDNA) metabarcoding data generation from freshwater, marine and terrestrial ecosystems. Research institutions worldwide progressively employ HTS for biodiversity assessments, new species discovery and ecological trend monitoring. Moreover, even non-scientists can now collect an eDNA sample, send it to a specialized laboratory for analysis and receive in-depth biodiversity record from a sampling site. This offers unprecedented opportunities for biodiversity assessments across wide temporal and spatial scales. The large volume of data produced by metabarcoding also enables incidental detection of species of concern, including non-indigenous and pathogenic organisms. We introduce an online app-Pest Alert Tool-for screening nuclear small subunit 18S ribosomal RNA and mitochondrial cytochrome oxidase subunit I datasets for marine non-indigenous species as well as unwanted and notifiable marine organisms in New Zealand. The output can be filtered by minimum length of the query sequence and identity match. For putative matches, a phylogenetic tree can be generated through the National Center for Biotechnology Information's BLAST Tree View tool, allowing for additional verification of the species of concern detection. The Pest Alert Tool is publicly available at https://pest-alert-tool-prod.azurewebsites.net/.


Asunto(s)
Código de Barras del ADN Taxonómico , ADN Ambiental , Ecosistema , Especies Introducidas , Biodiversidad , Internet , Filogenia , Ensayos Analíticos de Alto Rendimiento , ADN Ambiental/análisis , Aplicaciones Móviles
2.
Bioscience ; 73(7): 494-512, 2023 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-37560322

RESUMEN

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.

3.
Biofouling ; 39(4): 427-443, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37341323

RESUMEN

Complex microbial communities colonize plastic substrates over time, strongly influencing their fate and potential impacts on marine ecosystems. Among the first colonizers, diatoms play an important role in the development of this 'plastiphere'. We investigated 936 biofouling samples and the factors influencing diatom communities associated with plastic colonization. These factors included geographic location (up to 800 km apart), duration of substrate submersion (1 to 52 weeks), plastics (5 polymer types) and impact of artificial ageing with UV light. Diatom communities colonizing plastic debris were primarily determined by their geographic location and submersion time, with the strongest changes occurring within two weeks of submersion. Several taxa were identified as early colonizers (e.g. Cylindrotheca, Navicula and Nitzschia spp.) with known strong adhesion capabilities. To a lesser extent, plastic-type and UV-ageing significantly affected community composition, with 14 taxa showing substrate-specificity. This study highlights the role of plastics types-state for colonization in the ocean.


Asunto(s)
Diatomeas , Plásticos , Plásticos/química , Ecosistema , Biopelículas , Análisis Espacio-Temporal
4.
Mol Ecol ; 30(20): 5137-5150, 2021 10.
Artículo en Inglés | MEDLINE | ID: mdl-34379827

RESUMEN

Opportunities to study community-level responses to extreme natural pulse disturbances in unaltered ecosystems are rare. Lake sediment records that span thousands of years can contain well-resolved sediment pulses, triggered by earthquakes. These palaeorecords provide a means to study repeated pulse disturbances and processes of resistance (insensitivity to disturbance) and ecological resilience (capacity to regain structure, function and process). In this study, sedimentary DNA was extracted from a sediment core from Lake Paringa (New Zealand) that is situated in a near natural catchment. Metabarcoding and inferred functions were used to assess the lake microbial community over the past 1100 years - a period that included four major earthquakes. Microbial community composition and function differed significantly between highly perturbed (postseismic, ~50 years) phases directly after the earthquakes and more stable (interseismic, ~250 years) phases, indicating a lack of community resistance. Although community structure differed significantly in successive postseismic phases, function did not, suggesting potential functional redundancy. Significant differences in composition and function in successive interseismic phases demonstrate that communities are not resilient to large-scale natural pulse disturbances. The clear difference in structure and function, and high number of indicator taxa (responsible for driving differences in communities between phases) in the fourth interseismic phase probably represents a regime shift, possibly due to the two-fold increase in sediment and terrestrial biospheric organic carbon fluxes recorded following the fourth earthquake. Large pulse disturbances that enhance sediment inputs into lake systems may produce an underappreciated mechanism that destabilises lake ecosystem processes.


Asunto(s)
Lagos , Microbiota , Ciclo del Carbono , Ecosistema , Microbiota/genética , Nueva Zelanda
5.
Microb Ecol ; 81(1): 36-51, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32803362

RESUMEN

Seasonally nitrogen-limited and phosphorus-replete temperate coastal waters generally host dense and diverse diazotrophic communities. Despite numerous studies in marine systems, little is known about diazotrophs and their functioning in oligohaline estuarine environments. Here we applied a combination of nifH transcript and metagenomic shotgun sequencing approaches to investigate temporal shifts in taxonomic composition and nifH activity of size-fractionated diazotrophic communities in a shallow and mostly freshwater coastal lagoon. Patterns in active nifH phylotypes exhibited a clear seasonal succession, which reflected their different tolerances to temperature change and nitrogen (N) availability. Thus, in spring, heterotrophic diazotrophs (Proteobacteria) dominated the nifH phylotypes, while increasing water temperature and depletion of inorganic N fostered heterocystous Cyanobacteria in summer. Metagenomic data demonstrated four main N-cycling pathways and three of them with a clear seasonal pattern: denitrification (spring) → N2 fixation (summer) → assimilative NO3- reduction (fall), with NH4+ uptake into cells occurring across all seasons. Although a substantial denitrification signal was observed in spring, it could have originated from the re-suspended benthic rather than planktonic community. Our results contribute to a better understanding of the realized genetic potential of pelagic N2 fixation and its seasonal dynamics in oligohaline estuarine ecosystems, which are natural coastal biogeochemical reactors.


Asunto(s)
Cianobacterias/genética , Cianobacterias/metabolismo , Agua Dulce/microbiología , Ciclo del Nitrógeno/fisiología , Fijación del Nitrógeno/fisiología , ADN Ambiental/genética , Estuarios , Procesos Heterotróficos , Microbiota , Oxidorreductasas/genética , Filogenia , ARN/genética , Estaciones del Año , Microbiología del Agua
6.
Environ Sci Technol ; 54(13): 8443-8454, 2020 07 07.
Artículo en Inglés | MEDLINE | ID: mdl-32436694

RESUMEN

In this study, the evolution of ballast water (BW) assemblages across different trophic levels was characterized over a 21 day cross-latitudinal vessel transit using a combination of molecular methods. Triplicate BW samples were collected every second day and size-fractionated (<2.7, 10, >50 µm). Measurements of adenosine triphosphate (ATP) and metabarcoding of environmental nucleic acid (DNA and RNA) analyses, complemented by microscopy and flow cytometry, were performed on each sample. Measured ATP concentrations exhibited high variance between replicates and a strong negative trend in the large (≥50 µm) fraction over the voyage. In concert with microscopy, the metabarcoding data indicated a die-off of larger metazoans during the first week of study and gradual reductions in dinoflagellates and ochrophytes. The ATP and metabarcoding data signaled persistent or increased cellular activity of heterotrophic bacteria and protists in the BW, which was supported by flow cytometry. The metabarcoding showed the presence of active bacteria in all size fractions, suggesting that the sequential filtration approach does not ensure taxonomical differentiation, which has implications for BW quality assessment. Although our data show that ATP and metabarcoding have potential for indicative BW screening for BW compliance monitoring, further research and technological development is needed to improve representativeness of sampling and deliver the unequivocal response criteria required by the international Ballast Water Management Convention.


Asunto(s)
Navíos , Agua , Bacterias/genética , Biodiversidad , ADN , Agua/análisis
7.
Genome ; 62(3): 137-146, 2019 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-30278148

RESUMEN

Molecular techniques may provide effective tools to enhance marine biosecurity surveillance. Prior to routine implementation, evidence-based consideration of their benefits and limitations is needed. In this study, we assessed the efficiency and practicality of visual diver surveys and real-time PCR assays (targeting DNA and RNA) for detecting two marine invasive species whose infestation levels varied between species and location: Sabella spallanzanii and Styela clava. Filtered water samples (n = 171) were collected in parallel with dive surveys at two locations as part of the New Zealand Marine High Risk Site Surveillance programme: Nelson Harbour (27 sites) and Waitemata Harbour (30 sites). Diver surveys resulted in a greater number of detections compared to real-time PCR: S. clava - 21 versus 5 sites in Nelson, 6 versus 1 in Auckland; S. spallanzanii - 18 versus 10 in Auckland, no detections in Nelson. Occupancy modelling derived detection probabilities for the real-time PCR for S. clava were low (14%), compared to S. spallanzanii (66%). This could be related to abundances, or species-specific differences in DNA shedding. Only one RNA sample was positive, suggesting that most detections were from extracellular DNA or non-viable fragments. While molecular methods cannot yet replace visual observations, this study shows they provide useful complementary information.


Asunto(s)
ADN/genética , Monitoreo del Ambiente/métodos , Especies Introducidas , Poliquetos/genética , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Urocordados/genética , Animales , ADN/análisis , Nueva Zelanda , Medidas de Seguridad
8.
Biofouling ; 34(6): 657-672, 2018 07.
Artículo en Inglés | MEDLINE | ID: mdl-30185057

RESUMEN

Metabarcoding and metabolomics were used to explore the taxonomic composition and functional diversity of eukaryotic biofouling communities on plates with antifouling paints at two French coastal sites: Lorient (North Eastern Atlantic Ocean; temperate and eutrophic) and Toulon (North-Western Mediterranean Sea; mesotrophic but highly contaminated). Four distinct coatings were tested at each site and season for one month. Metabarcoding showed biocidal coatings had less impact on eukaryotic assemblages compared to spatial and temporal effects. Ciliophora, Chlorophyceae or Cnidaria (mainly hydrozoans) were abundant at Lorient, whereas Arthropoda (especially crustaceans), Nematoda, and Ochrophyta dominated less diversified assemblages at Toulon. Seasonal shifts were observed at Lorient, but not Toulon. Metabolomics also showed clear site discrimination, but these were associated with a coating and not season dependent clustering. The meta-omics analysis enabled identifications of some associative patterns between metabolomic profiles and specific taxa, in particular those colonizing the plates with biocidal coatings at Lorient.


Asunto(s)
Incrustaciones Biológicas , Metabolómica , Cilióforos/fisiología , Estaciones del Año
9.
Ecol Indic ; 72: 215-224, 2017 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-28149199

RESUMEN

Wide-ranging, indicator-based assessments of large, complex ecosystems are playing an increasing role in guiding environmental policy and management. An example is the EU's Marine Strategy Framework Directive, which requires Member States to take measures to reach "good environmental status" (GES) in European marine waters. However, formulation of indicator targets consistent with the Directive's high-level policy goal of sustainable use has proven challenging. We develop a specific, quantitative interpretation of the concepts of GES and sustainable use in terms of indicators and associated targets, by sharply distinguishing between current uses to satisfy current societal needs and preferences, and unknown future uses. We argue that consistent targets to safeguard future uses derive from a requirement that any environmental state indicator should recover within a defined time (e.g. 30 years) to its pressure-free range of variation when all pressures are hypothetically removed. Within these constraints, specific targets for current uses should be set. Routes to implementation of this proposal for indicators of fish-community size structure, population size of selected species, eutrophication, impacts of non-indigenous species, and genetic diversity are discussed. Important policy implications are that (a) indicator target ranges, which may be wider than natural ranges, systematically and rationally derive from our proposal; (b) because relevant state indicators tend to respond slowly, corresponding pressures should also be monitored and assessed;

10.
Biofouling ; 32(6): 671-84, 2016 07.
Artículo en Inglés | MEDLINE | ID: mdl-27212415

RESUMEN

In this experimental study the patterns in early marine biofouling communities and possible implications for surveillance and environmental management were explored using metabarcoding, viz. 18S ribosomal RNA gene barcoding in combination with high-throughput sequencing. The community structure of eukaryotic assemblages and the patterns of initial succession were assessed from settlement plates deployed in a busy port for one, five and 15 days. The metabarcoding results were verified with traditional morphological identification of taxa from selected experimental plates. Metabarcoding analysis identified > 400 taxa at a comparatively low taxonomic level and morphological analysis resulted in the detection of 25 taxa at varying levels of resolution. Despite the differences in resolution, data from both methods were consistent at high taxonomic levels and similar patterns in community shifts were observed. A high percentage of sequences belonging to genera known to contain non-indigenous species (NIS) were detected after exposure for only one day.


Asunto(s)
Incrustaciones Biológicas , Biología Computacional/métodos , Código de Barras del ADN Taxonómico/métodos , Monitoreo del Ambiente/métodos , Eucariontes , Sedimentos Geológicos , Biodiversidad , Eucariontes/clasificación , Eucariontes/genética , Sedimentos Geológicos/análisis , Nueva Zelanda , ARN Ribosómico 18S/genética
11.
J Environ Manage ; 181: 8-15, 2016 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-27294675

RESUMEN

In the marine sciences an increasing number of studies on environmental changes, their causes, and environmental assessments emerged in recent years. Often authors use non-uniform and inconsistent definitions of key terms like driver, threats, pressures etc. Although all of these studies clearly define causal dependencies between the interacting socio-economic and environmental systems in an understandable way, still an overall imprecise wording could induce misunderstanding at higher policy levels when it comes to integrated ecosystems assessments. Therefore we recommend using unified definitions for a better communication between science and management within national, regional and international environmental policies, for example the European Marine Strategy Framework Directive (MSFD). With this article we provide definitions compatible with the driver-pressure-state-impact-response (DPSIR) approach. Although most examples are MSFD related and thus have a marine focus the definitions are intended to be equally applicable for other systems and are usable world-wide. We suggest sticking to these definitions for an easy and simplified knowledge transfer from science to management, since DPSIR model is already accepted as a helpful tool for structuring and communicating ecosystem analyses.


Asunto(s)
Conservación de los Recursos Naturales , Política Ambiental , Océanos y Mares , Terminología como Asunto , Humanos
12.
Biofouling ; 31(3): 241-51, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25877857

RESUMEN

Marine biofilms are precursors for colonization by larger fouling organisms, including non-indigenous species (NIS). In this study, high-throughput sequencing (HTS) of 18S rRNA metabarcodes was used to investigate four sampling methods (modified syringe, sterilized sponge, underwater tape and sterilized swab) for characterizing eukaryotic communities in marine biofilms. Perspex™ plates were sampled in and out of water. DNA collected with tape did not amplify. Otherwise, there were no statistical differences in communities among the remaining three sampling devices or between the two environments. Sterilized sponges are recommended for ease of use underwater. In-depth HTS analysis identified diverse eukaryotic communities, dominated by Metazoa and Chromoalveolata. Among the latter, diatoms (Bacillariophyceae) were particularly abundant (33% of reads assigned to Chromalveolata). The NIS Ciona savignyi was detected in all samples. The application of HTS in marine biofilm surveillance could facilitate early detection of NIS, improving the probability of successful eradication.


Asunto(s)
Biopelículas , ADN/aislamiento & purificación , Secuenciación de Nucleótidos de Alto Rendimiento , Animales , Biodiversidad , Biología Computacional , Código de Barras del ADN Taxonómico , Diatomeas , Filogenia , ARN Ribosómico 18S/genética , Agua de Mar , Análisis de Secuencia de ADN , Urocordados
13.
Ecol Evol ; 14(3): e10984, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38505176

RESUMEN

The increasing spread of marine non-indigenous species (NIS) due to the growth in global shipping traffic is causing widespread concern for the ecological and economic impacts of marine bioinvasions. Risk management authorities need tools to identify pathways and source regions of priority concern to better target efforts for preventing NIS introduction. The probability of a successful NIS introduction is affected by the likelihood that a marine species entrained in a transport vector will survive the voyage between origin and destination locations and establish an independently reproducing population at the destination. Three important risk factors are voyage duration, range of environmental conditions encountered during transit and environmental similarity between origin and destination. In this study, we aimed for a globally comprehensive approach to assembling quantifications of source-destination risk factors from every potential origin to every potential destination. To derive estimates of voyage-related marine biosecurity risk, we used computer-simulated vessel paths between pairs of ecoprovinces in the Marine Ecoregions Of the World biogeographic classification system. We used the physical length of each path to calculate voyage duration risk and the cross-latitudinal extent of the path to calculate voyage path risk. Environmental similarity risk was based on comparing annual average sea surface temperature and salinity within each ecoprovince to those of other ecoprovinces. We derived three separate sets of risk quantifications, one each for voyage duration, voyage path and environmental similarity. Our quantifications can be applied to studies that require source-destination risk estimates. They can be used separately or combined, depending on the importance of the types of source-destination risks that might be relevant to particular scientific or risk management questions or applications.

14.
PeerJ ; 12: e16969, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38410796

RESUMEN

Molecular biomonitoring programs increasingly use environmental DNA (eDNA) for detecting targeted species such as marine non-indigenous species (NIS) or endangered species. However, the current molecular detection workflow is cumbersome and time-demanding, and thereby can hinder management efforts and restrict the "opportunity window" for rapid management responses. Here, we describe a direct droplet digital PCR (direct-ddPCR) approach to detect species-specific free-floating extra-cellular eDNA (free-eDNA) signals, i.e., detection of species-specific eDNA without the need for filtration or DNA extraction, with seawater samples. This first proof-of-concept aquarium study was conducted with three distinct marine species: the Mediterranean fanworm Sabella spallanzanii, the ascidian clubbed tunicate Styela clava, and the brown bryozoan Bugula neritina to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analysing aquarium marine water samples using an optimized species-specific ddPCR assay. The results demonstrated the consistent detection of S. spallanzanii and B. neritina free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 h. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. This study represents the first step in assessing the feasibility of direct-ddPCR technology for the detection of marine species. Our results provide information that could aid in the development of new technology, such as a field development of ddPCR systems, which could allow for automated continuous monitoring of targeted marine species, enabling point-of-need detection and rapid management responses.


Asunto(s)
Briozoos , Urocordados , Animales , Reacción en Cadena de la Polimerasa/métodos , Monitoreo Biológico , Agua de Mar , Urocordados/genética
15.
Sci Total Environ ; 917: 170301, 2024 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-38272094

RESUMEN

The fragmentation of plastic debris is a key pathway to the formation of microplastic pollution. These disintegration processes depend on the materials' physical and chemical characteristics, but insight into these interrelationships is still limited, especially under natural conditions. Five plastics of known polymer/additive compositions and processing histories were deployed in aquatic environments and recovered after six and twelve months. The polymer types used were linear low density polyethylene (LLDPE), oxo-degradable LLDPE (oxoLLDPE), poly(ethylene terephthalate) (PET), polyamide-6 (PA6), and poly(lactic acid) (PLA). Four geographically distinct locations across Aotearoa/New Zealand were chosen: three marine sites and a wastewater treatment plant (WWTP). Accelerated UV-weathering under controlled laboratory conditions was also carried out to evaluate artificial ageing as a model for plastic degradation in the natural environment. The samples' physical characteristics and surface microstructures were studied for each deployment location and exposure time. The strongest effects were found for oxoLLDPE upon artificial ageing, with increased crystallinity, intense surface cracking, and substantial deterioration of its mechanical properties. However, no changes to the same extent were found after recovery of the deployed material. In the deployment environments, the chemical nature of the plastics was the most relevant factor determining their behaviours. Few significant differences between the four aquatic locations were identified, except for PA6, where indications for biological surface degradation were found only in seawater, not the WWTP. In some cases, artificial ageing reasonably mimicked the changes which some plastic properties underwent in aquatic environments, but generally, it was no reliable model for natural degradation processes. The findings from this study have implications for the understanding of the initial phases of plastic degradation in aquatic environments, eventually leading to microplastics formation. They can also guide the interpretation of accelerated laboratory ageing for the fate of aquatic plastic pollution, and for the testing of aged plastic samples.

16.
Sci Total Environ ; 854: 158758, 2023 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-36113796

RESUMEN

The vast majority of globally traded cargo is transported via maritime shipping. Whilst in port for loading and unloading, these ships can pick up local marine organisms with internal ballast water or as external biofouling assemblages and subsequently move these to destination far beyond their natural ranges. Over the past decades, this mechanism has led to the establishment of hundreds of non-indigenous species (NIS) around global coastlines. Marine NIS cause significant environmental, economic, cultural and human health impacts. Taking effective steps to preventing their dispersal and establishment is an enduring challenge for governments and conservation agencies around the world. Here we use international commodity trade data and a Nobel-Prize-winning economic analysis technique to develop a novel approach for assessing global marine NIS transfer risks. We show that by tracing the origins and destinations of seaborne trade connections, and the nature of the traded commodities, we can predict the strength of shipping vectors and associated marine biosecurity risks. We demonstrate the utility of our approach via a case-study, where we trace the spread of a hypothetical marine NIS from Japan and show the congruence of our model results with documented invasion histories from that region. Our study demonstrates that biosecurity risk can be assessed using established economic modelling frameworks on the basis of monetary transaction data alone, and without the need for detailed itineraries of the many thousand vessels making up the global commercial fleet. Novel, cost-effective tools are needed to mitigate biosecurity risks associated with maritime trade, and to meet conservation goals while enabling economic prosperity. The modelling framework presented here can be expanded to incorporate future risk factors, life-history traits of particular NIS of concern, and even adapted to simulate the dispersal of terrestrial pests or disease agents.


Asunto(s)
Incrustaciones Biológicas , Especies Introducidas , Humanos , Bioaseguramiento , Navíos , Organismos Acuáticos
17.
Sci Total Environ ; 858(Pt 2): 159975, 2023 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-36347283

RESUMEN

Ecosystem services (ES) are the benefits natural ecosystems provide to society, such as food provisioning, water supply, climate regulation and recreational benefits. Biological invasions are a major driver of global change, and several non-indigenous species (NIS) may alter key ecological feedbacks with ultimate consequences to ES, livelihoods and human wellbeing. Nonetheless, the effects of NIS on ES supply remain largely unquantified. Here we present the first quantitative case study assessing the impacts of widespread NIS on ES in the Baltic Sea, by developing and employing a robust and repeatable data-driven approach. All NIS with a sufficient knowledge base pose large and highly significant effects on ES, resulting on average 55 % change in the intensity of ES. Most impacts affected regulation services, concerning both abiotic and biotic realms, with little evidence on cultural and provisioning services. The methodology can be easily employed beyond the current study realm e.g. to better understand the roles of human pressures on ES in any ecosystem. Importantly, the study also identified major biases not only in the availability of taxonomic and sub-regional evidence, but also in the different study types employed to create the evidence base.


Asunto(s)
Efectos Antropogénicos , Ecosistema , Especies Introducidas , Humanos , Clima , Conservación de los Recursos Naturales , Océanos y Mares
18.
Mol Ecol Resour ; 23(2): 440-452, 2023 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-36226834

RESUMEN

Environmental DNA (eDNA) analyses are powerful for describing marine biodiversity but must be optimized for their effective use in routine monitoring. To maximize eDNA detection probabilities of sparsely distributed populations, water samples are usually concentrated from larger volumes and filtered using fine-pore membranes, often a significant cost-time bottleneck in the workflow. This study aimed to streamline eDNA sampling by investigating plankton net versus bucket sampling, direct versus sequential filtration including self-preserving filters. Biodiversity was assessed using metabarcoding of the small ribosomal subunit (18S rRNA) and mitochondrial cytochrome c oxidase I (COI) genes. Multispecies detection probabilities were estimated for each workflow using a probabilistic occupancy modelling approach. Significant workflow-related differences in biodiversity metrics were reported. Highest amplicon sequence variant (ASV) richness was attained by the bucket sampling combined with self-preserving filters, comprising a large portion of microplankton. Less diversity but more metazoan taxa were captured in the net samples combined with 5 µm pore size filters. Prefiltered 1.2 µm samples yielded few or no unique ASVs. The highest average (~32%) metazoan detection probabilities in the 5 µm pore size net samples confirmed the effectiveness of preconcentration plankton for biodiversity screening. These results contribute to streamlining eDNA sampling protocols for uptake and implementation in marine biodiversity research and surveillance.


Asunto(s)
ADN Ambiental , Animales , ADN Ambiental/genética , ADN Ambiental/análisis , Código de Barras del ADN Taxonómico/métodos , Biodiversidad , Plancton/genética , Monitoreo del Ambiente/métodos
19.
Sci Rep ; 13(1): 17061, 2023 10 10.
Artículo en Inglés | MEDLINE | ID: mdl-37816793

RESUMEN

Aotearoa New Zealand's Northern region is a major gateway for the incursion and establishment of non-indigenous species (NIS) populations due to high numbers of recreational and commercial vessels. This region also holds a unique marine ecosystem, home to many taonga (treasured) species of cultural and economic importance. Regular surveillance, eradication plans and public information sharing are undertaken by local communities and governmental organizations to protect these ecosystems from the impact of NIS. Recently, considerable investments went into environmental DNA (eDNA) research, a promising approach for the early detection of NIS for complementing existing biosecurity systems. We applied eDNA metabarcoding for elucidating bioregional patterns of NIS distributions across a gradient from harbors (NIS hotspots) to open seas (spreading areas). Samples were collected during a research cruise sailing across three Aotearoa New Zealand harbors, Waitemata, Whangarei and Pewhairangi (Bay of Islands), and their adjacent coastal waters. The small-ribosomal subunit (18S rRNA) and mitochondrial cytochrome c oxidase I (COI) genes were screened using the online Pest Alert Tool for automated detection of putative NIS sequences. Using a probabilistic modelling approach, location-dependent occupancies of NIS were investigated and related to the current information on species distribution from biosecurity surveillance programs. This study was collaboratively designed with Maori partners to initiate a model of co-governance within the existing science system.


Asunto(s)
Conservación de los Recursos Naturales , ADN Ambiental , ADN Ambiental/genética , Ecosistema , Nueva Zelanda , Océanos y Mares
20.
CRISPR J ; 6(4): 316-324, 2023 08.
Artículo en Inglés | MEDLINE | ID: mdl-37439822

RESUMEN

Almost all of Earth's oceans are now impacted by multiple anthropogenic stressors, including the spread of nonindigenous species, harmful algal blooms, and pathogens. Early detection is critical to manage these stressors effectively and to protect marine systems and the ecosystem services they provide. Molecular tools have emerged as a promising solution for marine biomonitoring. One of the latest advancements involves utilizing CRISPR-Cas technology to build programmable, rapid, ultrasensitive, and specific diagnostics. CRISPR-based diagnostics (CRISPR-Dx) has the potential to allow robust, reliable, and cost-effective biomonitoring in near real time. However, several challenges must be overcome before CRISPR-Dx can be established as a mainstream tool for marine biomonitoring. A critical unmet challenge is the need to design, optimize, and experimentally validate CRISPR-Dx assays. Artificial intelligence has recently been presented as a potential approach to tackle this challenge. This perspective synthesizes recent advances in CRISPR-Dx and machine learning modeling approaches, showcasing CRISPR-Dx potential to progress as a rising molecular tool candidate for marine biomonitoring applications.


Asunto(s)
Sistemas CRISPR-Cas , Aprendizaje Profundo , Sistemas CRISPR-Cas/genética , Edición Génica , ARN , Inteligencia Artificial , Monitoreo Biológico , Ecosistema
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