A taxonomy-free diatom eDNA-based technique for assessing lake trophic level using lake sediments.

Anthropogenic eutrophication is one of the most pressing issues facing lakes globally. Our ability to manage lake eutrophication is hampered by the limited spatial and temporal extents of monitoring records, stemming from the time-consuming and expensive nature of physiochemical and biological monitoring. Diatom-based biomonitoring presents an alternative to traditional eutrophication monitoring, yet it is restricted by the high degree of taxonomic expertise required. Environmental DNA metabarcoding, while providing a promising substitute for diatom community enumeration, is plagued by inadequate taxonomic coverage of reference databases and methodological bias, limiting its use for biomonitoring. Here we show that taxonomy-free diatom-biomonitoring, in which environmental DNA metabarcoding data is utilised but not assigned to specific taxonomic classes, presents an accurate, fast, and relatively automated alternative to taxonomically assigned eutrophication biomonitoring. Our taxonomy-free index accounted for 85% of trophic level variability across 89 lakes and had the lowest average prediction error of the three approaches tested. By not relying on taxonomic identification or metabarcoding reference databases, taxonomy-free biomonitoring maintains diatom diversity that is lost in taxonomic assignment using molecular approaches. Furthermore, by utilising lake sediments, the approach outlined here presents a time-integrated estimation of lake trophic level and thus does not require time-consuming seasonal sampling. Taxonomy-free biomonitoring addresses the limitations of traditional physicochemical eutrophication monitoring and taxonomic biomonitoring alternatives and can be used to extend the spatial and temporal extents of eutrophication monitoring.

Desiccation as a mitigation tool to manage biofouling risks: trials on temperate taxa to elucidate factors influencing mortality rates.

The desiccation tolerance of biofouling taxa (adults and early life-stages) was determined under both controlled and 'realistic' field conditions. Adults of the ascidian Ciona spp. died within 24 h. Mortality in the adult blue mussel Mytilus galloprovincialis occurred within 11 d under controlled conditions, compared with 7 d when held outside. The Pacific oyster Crassostrea gigas was the most desiccation-tolerant taxon tested (up to 34 d under controlled conditions). Biofouling orientated to direct sunlight showed faster mortality rates for all the taxa tested. Mortality in Mytilus juveniles took up to 24 h, compared with 8 h for Ciona, with greater survival at the higher temperature (18.5°C) and humidity (~95% RH) treatment combination. This study demonstrated that desiccation can be an effective mitigation method for a broad range of fouling taxa, especially their early life-stages. Further work is necessary to assess risks from other high-risk species such as algae and cyst forming species.

It's a wrap: encapsulation as a management tool for marine biofouling.

Encapsulation of fouled structures is an effective tool for countering incursions by non-indigenous biofoulers. However, guidelines for the implementation of encapsulation treatments are yet to be established. This study evaluated the effects of temperature, biomass, community composition, treatment duration and the biocide acetic acid on biofoulers. In laboratory trials using the model organisms Ciona spp. and Mytilus galloprovincialis, increasing the temperature or biomass speeded up the development of a toxic environment. Total mortality for Ciona spp. occurred within 72 and 24 h at 10 and 19°C, respectively. M. galloprovincialis survived up to 18 days, with high biomass increasing mortality at 10°C only. In a field study, three-month-old and four-year-old communities were encapsulated with and without acetic acid. Mortality took up to 10 days for communities encapsulated without acetic acid, compared to 48 h with acetic acid. The insights gained from this study will be useful in developing standardised encapsulation protocols.

Factors influencing the en route survivorship and post-voyage growth of a common ship biofouling organism, Bugula neritina.

The likelihood that viable non-indigenous biofouling species will survive a voyage on a vessel is influenced by a range of factors, including the speed, duration, and route of the voyage and the amount of time the vessel spends in port. In this study, a land-based dynamic flow device was used to test the effect of recruit age, vessel speed and voyage duration on the survivorship and growth of the bryozoan Bugula neritina. In the experiment, one-week-old recruits had a higher likelihood (100%) of surviving voyages than older (one-month-old, 90%) or younger (one-day-old, 79%) recruits, but survival was not influenced by vessel speed (6 and 18 knots) or voyage duration (two and eight days). The results suggest that the non-indigenous species B. neritina can be effectively transferred at a range of ages but one-week-old recruits are more likely to survive the translocation process and survive in the recipient environment.

Potential biocontrol agents for biofouling on artificial structures.

The accumulation of biofouling on coastal structures can lead to operational impacts and may harbour problematic organisms, including non-indigenous species. Benthic predators and grazers that can supress biofouling, and which are able to be artificially enhanced, have potential value as augmentative biocontrol agents. The ability of New Zealand native invertebrates to control biofouling on marina pontoons and wharf piles was tested. Caging experiments evaluated the ability of biocontrol to mitigate established biofouling, and to prevent fouling accumulation on defouled surfaces. On pontoons, the gastropods Haliotis iris and Cookia sulcata reduced established biofouling cover by >55% and largely prevented the accumulation of new biofouling over three months. On wharf piles C. sulcata removed 65% of biofouling biomass and reduced its cover by 73%. C. sulcata also had better retention and survival rates than other agents. Augmentative biocontrol has the potential to be an effective method to mitigate biofouling on marine structures.

Domesticating the wild through escapees of two iconic mediterranean farmed fish species.

Extractive fisheries and marine aquaculture share space and target species. Several regional-scale examples exist of escapees entering wild fisheries landings, yet no study has assessed the influence of aquaculture on landings at an ecosystem scale. We examined the effects of farmed fish escapes on fisheries using FAO data and published escape rates for Gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax). Seabream landings were significantly correlated with the estimated biomass of escaped seabream entering the wild. There was a similar pattern for seabass until 2005, but the overall relationship between landings and escapes was not significant due to the dramatic drop in catches in recent years. We argue that seabass escapees' relatively high mortality, lower capturability, and minor 'leaking' from farms may obscure their influence on landings. Significant positive fisheries regime shifts were detected for both species, matching the onset of aquaculture in the Mediterranean and the period when escapees from aquaculture surpassed landings. Our results suggest that fish escapes of these two iconic species may mask wild stock overexploitation, confound stock assessments, alter genetic diversity, increase the risk of spreading pathogens and parasites, and compete with wild conspecifics while boosting fisheries landings.

Sedimentary ancient DNA reveals the impact of anthropogenic land use disturbance and ecological shifts on fish community structure in small lowland lake.

Freshwater fish biodiversity and abundance are decreasing globally. The drivers of decline are primarily anthropogenic; however, the causative links between disturbances and fish community change are complex and challenging to investigate. We used a suite of sedimentary DNA methods (droplet digital PCR and metabarcoding) and traditional paleolimnological approaches, including pollen and trace metal analysis, ITRAX X-ray fluorescence and hyperspectral core scanning to explore changes in fish abundance and drivers over 1390 years in a small lake. This period captured a disturbance trajectory from pre-human settlement through subsistence living to intensive agriculture. Generalized additive mixed models explored the relationships between catchment inputs, internal drivers, and fish community structure. Fish community composition distinctly shifted around 1350 CE, with the decline of a sensitive Galaxias species concomitant with early land use changes. Total fish abundance significantly declined around 1950 CE related to increases in ruminant bacterial DNA (a proxy for ruminant abundance) and cadmium flux (a proxy for phosphate fertilizers), implicating land use intensification as a key driver. Concurrent shifts in phytoplankton and zooplankton suggested that fish communities were likely impacted by food web dynamics. This study highlights the potential of sedDNA to elucidate the long-term disturbance impacts on biological communities in lakes.

Evaluation of the sea anemone Anthothoe albocincta as an augmentative biocontrol agent for biofouling on artificial structures.

Augmentative biocontrol, defined as the use of indigenous natural enemies to control pest populations, has not been explored extensively in marine systems. This study tested the potential of the anemone Anthothoe albocincta as a biocontrol agent for biofouling on submerged artificial structures. Biofouling biomass was negatively related to anemone cover. Treatments with high anemone cover (>35%) led to significant changes in biofouling assemblages compared to controls. Taxa that contributed to these changes differed among sites, but included reductions in cover of problematic fouling organisms, such as solitary ascidians and bryozoans. In laboratory trials, A. albocincta substantially prevented the settlement of larvae of the bryozoan Bugula neritina when exposed to three levels of larval dose, suggesting predation as an important biocontrol mechanism, in addition to space pre-emption. This study demonstrated that augmentative biocontrol using anemones has the potential to reduce biofouling on marine artificial structures, although considerable further work is required to refine this tool before its application.

Paleo-diatom records reveal ecological change not detected using traditional measures of lake eutrophication.

Lakes provide crucial ecosystem services and harbour unique and rich biodiversity, yet despite decades of research and management focus, cultural eutrophication remains a predominant threat to their health. Our ability to manage lake eutrophication is restricted by the lack of long-term monitoring records. To circumvent this, we developed a bio-indicator approach for inferring trophic level from lake diatom communities and applied this to sediment cores from two lakes experiencing eutrophication stress. Diatom indicators strongly predicted observed trophic levels, and when applied to sediment cores, diatom predicted trophic level reconstructions were consistent with monitoring data and land-use histories. However, there were significant recent shifts in diatom communities not captured by the diatom-based index or monitoring data, suggesting that conventional trophic level indices obscure important ecological change. New approaches, such as the one in this study, are critical to detect early changes in water quality and prevent the decline of lake ecosystems worldwide.

Toward integrated pest management in bivalve aquaculture.

Pests of bivalve aquaculture are a challenging problem that can reduce productivity, profitability and sustainability. A range of pest management approaches have been developed for bivalve aquaculture, but a general absence of guiding frameworks has limited the scale and permanency of implementation. Applying principles of 'integrated pest management' (IPM) could change this paradigm to improve economic and environmental outcomes. We reviewed existing research and tools for pest management in bivalve aquaculture, with studies grouped under five pillars of IPM: pest ecology (25 studies), bioeconomic cost-benefits (4 studies), continual monitoring (17 studies), proactive prevention (32 studies) and reactive control (65 studies). This body of knowledge, along with insights from terrestrial agriculture, provide a strong foundation for developing and implementing IPM in bivalve aquaculture. For example, IPM principles have been applied by a regional collective of oyster farmers in the US Pacific Northwest to optimize pesticide application and search for other options to control problematic burrowing shrimps. However, IPM has not yet been broadly applied in aquaculture, and data gaps and barriers to implementation need to be addressed. Priorities include establishing meaningful pest-crop bioeconomic relationships for various bivalve farming systems and improving the efficacy and operational scale of treatment approaches. An IPM framework also could guide potential step-change improvements through directing selective breeding for resistance to pests, development of bespoke chemical control agents, applying emerging technologies for remote surveillance and farm management, and regional alignment of management interventions. © 2022 Society of Chemical Industry.

Using metabarcoding and droplet digital PCR to investigate drivers of historical shifts in cyanobacteria from six contrasting lakes.

The frequency and intensity of cyanobacterial blooms is increasing worldwide. Multiple factors are implicated, most of which are anthropogenic. New Zealand provides a useful location to study the impacts of human settlement on lake ecosystems. The first humans (Polynesians) arrived about 750 years ago. Following their settlement, there were marked landscape modifications which intensified after European settlement about 150 years ago. The aims of this study were to reconstruct cyanobacterial communities in six lakes over the last 1000 years and explore key drivers of change. Cyanobacterial environmental DNA was extracted from sediment cores and analysed using metabarcoding and droplet digital PCR. Cyanobacteria, including potentially toxic or bloom forming species, were already present in these lakes prior to human arrival, however their overall abundance was low. Total cyanobacteria abundance and richness increased in all lakes after European settlement but was very pronounced in four lakes, where bloom-forming taxa became dominant. These shifts occurred concomitant with land-use change. The catchment of one deteriorated lake is only moderately modified, thus the introduction of non-native fish is posited as the key factor driving this change. The paleolimnological approach used in this study has enabled new insights into timing and potential causes of changes in cyanobacterial communities.

A bacterial index to estimate lake trophic level: National scale validation.

Lakes and their catchments have been subjected to centuries to millennia of exploitation by humans. Efficient monitoring methods are required to promote proactive protection and management. Traditional monitoring is time consuming and expensive, which limits the number of lakes monitored. Lake surface sediments provide a temporally integrated representation of environmental conditions and contain high microbial biomass. Based on these attributes, we hypothesized that bacteria associated with lake trophic states could be identified and used to develop an index that would not be confounded by non-nutrient stressor gradients. Metabarcoding (16S rRNA gene) was used to assess bacterial communities present in surface sediments from 259 non-saline lakes in New Zealand encompassing a range of trophic states from alpine microtrophic lakes to lowland hypertrophic lakes. A subset of lakes (n = 96) with monitoring data was used to identify indicator amplicon sequence variants (ASVs) associated with different trophic states. A total of 10,888 indicator taxa were identified and used to develop a Sediment Bacterial Trophic Index (SBTI), which signficantly correlated (r2 = 0.842, P < 0.001) with the Trophic Lake Index. The SBTI was then derived for the remaining 163 lakes, providing new knowledge of the trophic state of these unmonitored lakes. This new, robust DNA-based tool provides a rapid and cost-effective method that will allow a greater number of lakes to be monitored and more effectively managed in New Zealand and globally. The SBTI could also be applied in a paleolimnological context to investigate changes in trophic status over centuries to millennia.

Impacts of a putative invasive ascidian on rocky shore communities.

The number and distribution of non-indigenous species in coastal habitats is increasing. Our ability to prioritise the management of this threat is limited by our understanding of their impacts. We investigated the density dependent effects of the non-indigenous solitary ascidian Pyura doppelgangera on native mussels and rocky shore communities in northern New Zealand. Minimal recruitment of P. doppelgangera was recorded during a 1.5-year experiment. Mussels showed no sign of overgrowth or spatial competition with P. doppelgangera, and their physiological condition was not impacted. We found marginal effects of the ascidian on community development, associated with small increases in diversity. We concluded that P. doppelgangera is not an aggressive competitor nor a threat to native communities, as previously thought, and that it has a very limited natural recruitment and spread potential. Reports from local Maori and a literature review suggest that P. doppelgangera has been present in the area for longer than previously thought, raising questions about its 'introduction' status and its current designation as a pest.

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.

Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture.

Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between "distance" from the farm and "kit" in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.

Effect of substrate deployment timing and reproductive strategy on patterns in invasiveness of the colonial ascidian Didemnum vexillum.

The colonial ascidian Didemnum vexillum is a high-profile marine invader, with a geographically widespread distribution after introductions to several temperate regions. D. vexillum has been the focus of several eradication and control programmes globally and the need for specific biological knowledge that relates to establishment processes, persistence, impacts and potential for spread remains. The present study describes temporal patterns of D. vexillum percent cover on experimental substrates over 1.5-years in relation to seasonality of substratum availability, in conjunction with key physical (i.e. temperature and sedimentation) and biological factors (i.e. interspecific competition) at two sites in New Zealand. Colonies showed large fluctuations in percent cover between the two study sites and with reference to timing of bare substratum availability. Colonies generally exhibited an initial lag phase, with peak levels of D. vexillum cover reached during the second summer or autumn post-deployment. The long-term competitive dominance of colonies founded from the reattachment of fragments, as opposed to ambient larval recruitment alone, was also investigated. Increases in colony size as a result of ambient recruitment alone were initially much slower. However, after 12-months colony cover exceeded that of plates inoculated with fragments, suggesting the benefit of the apparent competitive dominance conferred by fragment inoculation is restricted to the early establishment phase. This information will provide increased understanding of the population dynamics of this species, as well as assist in the implementation of effective management strategies through knowledge of environmental drivers of prolific infestations.

Spatiotemporal dynamics of Phormidium cover and anatoxin concentrations in eight New Zealand rivers with contrasting nutrient and flow regimes.

Toxic benthic cyanobacterial proliferations, particularly of the genus Phormidium, are a major concern in many countries due to their increasing extent and severity. The aim of this study was to improve the current understanding of the dominant physicochemical variables associated with high Phormidium cover and toxin concentrations. Phormidium cover and anatoxin concentrations were assessed weekly for 30weeks in eight predominately cobble-bed rivers in the South Island of New Zealand. Phormidium cover was highly variable both spatially (among and within sites) and temporally. Generalized additive mixed models (GAMMs) identified site, month of the year, conductivity and nutrient concentrations over the accrual period as significant variables associated with Phormidium cover. Cover was greatest under low to intermediate accrual dissolved inorganic nitrogen (DIN) and dissolved reactive phosphorus (DRP) concentrations. Accrual nutrients had a strong, negative effect on cover at concentrations>0.2mgL-1 DIN and 0.014mgL-1 DRP. The effect of flow was generally consistent across rivers, with cover accruing with time since the last flushing flow. Total anatoxins were detected at all eight study sites, at concentrations ranging from 0.008 to 662.5mgkg-1 dried weight. GAMMs predicted higher total anatoxin concentrations between November and February and during periods of accrual DRP<0.02mgL-1. This study suggests that multiple physicochemical variables may influence Phormidium proliferations and also evidenced large site-to-site variability. This result highlights a challenge from a management perspective, as it suggests that mitigation options are likely to be site-specific.

Biocontrol of fouling pests: Effect of diversity, identity and density of control agents.

Augmentative biocontrol, using native natural enemies, has been suggested as a promising tool to control marine biofouling pests on artificial structures. However, there are still important knowledge gaps to be addressed before biocontrol can be considered as a management tool. In a field experiment on floating marine structures we examined intra- and interspecific consumer interactions among biocontrol agents on different surface orientations. We tested the effect of identity, density and diversity of three invertebrates (the 11-arm seastar Coscinasterias muricata, the sea urchin Evechinus chloroticus and the gastropod Cook's turban Cookia sulcata) to reduce established biofouling and to prevent fouling growth on defouled surfaces. High densities of biocontrol agents were not more effective at fouling control (cover and biomass) than low densities. Nor did multi-species treatments function more effectively than mono-specific ones. However, biocontrol agent identity was important, with the 11-arm seastar and Cook's turban being the most effective at fouling reduction and prevention, respectively. Surface orientation had a strong effect on the effectiveness of control agents, with the best results obtained on vertical compared to diagonal and underside surfaces. This study confirmed the potential of biocontrol as a management tool for marine pest, indicating that identity is more important than richness and density of control agents. It also highlighted the limitations of this approach on diagonal and underside surfaces, where control agents have limited retention ability.

Metamorphosis of the invasive ascidian Ciona savignyi: environmental variables and chemical exposure.

In this study, the effects of environmental variables on larval metamorphosis of the solitary ascidian Ciona savignyi were investigated in a laboratory setting. The progression of metamorphic changes were tracked under various temperature, photoperiod, substrate, larval density, and vessel size regimes. Metamorphosis was maximised at 18 °C, 12:12 h subdued light:dark, smooth polystyrene substrate, and 10 larvae mL(-1) in a twelve-well tissue culture plate. Eliminating the air-water interface by filling culture vessels to capacity further increased the proportion of metamorphosed larvae; 87 ± 5% of larvae completed metamorphosis within 5 days compared to 45 ± 5% in control wells. The effects of the reference antifouling compounds polygodial, portimine, oroidin, chlorothalonil, and tolylfluanid on C. savignyi were subsequently determined, highlighting (1) the sensitivity of C. savignyi metamorphosis to chemical exposure and (2) the potential to use C. savignyi larvae to screen for bioactivity in an optimised laboratory setting. The compounds were bioactive in the low ng mL(-1) to high µg mL(-1) range. Polygodial was chosen for additional investigations, where it was shown that mean reductions in the proportions of larvae reaching stage E were highly repeatable both within (repeatability = 14 ± 9%) and between (intermediate precision = 17 ± 3%) independent experiments. An environmental extract had no effect on the larvae but exposing larvae to both the extract and polygodial reduced potency relative to polygodial alone. This change in potency stresses the need for caution when working with complex samples, as is routinely implemented when isolating natural compounds from their biological source. Overall, the outcomes of this study highlight the sensitivity of C. savignyi metamorphosis to environmental variations and chemical exposure.

First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site.

At present, environmental impacts from offshore oil and gas activities are partly determined by measuring changes in macrofauna diversity. Morphological identification of macrofauna is time-consuming, expensive and dependent on taxonomic expertise. In this study, we evaluated the applicability of using foraminiferal-specific metabarcoding for routine monitoring. Sediment samples were collected along distance gradients from two oil platforms off Taranaki (New Zealand) and their physico-chemical properties, foraminiferal environmental DNA/RNA, and macrofaunal composition analyzed. Macrofaunal and foraminiferal assemblages showed similar shifts along impact gradients, but responded differently to environmental perturbations. Macrofauna were affected by hypoxia, whereas sediment grain size appeared to drive shifts in foraminifera. We identified eight foraminiferal molecular operational taxonomic units that have potential to be used as bioindicator taxa. Our results show that metabarcoding represents an effective tool for assessing foraminiferal communities near offshore oil and gas platforms, and that it can be used to complement current monitoring techniques.