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

Metabarcoding and co-occurrence network reveal significant effects of mariculture on benthic eukaryotic microalgal community: A case study in Daya Bay of the South China Sea

Benthic eukaryotic microalgae were analyzed by metabarcoding the partial 18S rRNA gene in Daya Bay bi-monthly in 2021. Altogether 941 eukaryotic microalgal OTUs were detected, belonging to 27 classes of 8 phyla. Dinophyta and Chlorophyta were the dominant phyla. Microalgal community in the mariculture zone differed significantly from those in non-mariculture zone, reflected by low alpha diversity indexes and increasing abundance and richness of chlorophytes and correspondingly decreasing of dinoflagellates. The abundant occurrences of the pico- and nano-sized taxa such as the chlorophyte Picochlorum in the mariculture zone suggested that nutrient enrichment might result in the miniaturization of the benthic eukaryotic microalgae. The co-occurrence network suggested more negative interactions between taxa in the mariculture zone. A total of 41 algal bloom and/or harmful algal bloom (HAB) species were detected in this study, suggesting a high potential risk of HABs in Daya Bay, especially for the recurrent bloom species Scrippsiella acuminata.

Validation of the Chemical and Biological Steps Required Implementing an Advanced Multi-Omics Approach for Assessing the Fate and Impact of Contaminants in Lagoon Sediments

The increasing use of chemicals requires a better understanding of their presence and dynamics in the environment, as well as their impact on ecosystems. The aim of this study was to validate the first steps of an innovative multi-omics approach based on metabolomics and 16S metabarcoding data for analyses of the fate and impact of contaminants in Mediterranean lagoons. Semi-targeted analytical procedures for water and sediment matrices were implemented to assess chemical contamination of the lagoon: forty-six compounds were detected, 28 of which could be quantified in water (between 0.09 and 47.4 ng/L) and sediment (between 0.008 and 26.3 ng/g) samples using the UHPLC-MS/MS instrument. In addition, a non-targeted approach (UHPLC-HRMS) using four different sample preparation protocols based on solid/liquid extractions or an automated pressurized fluid extraction system (EDGE®) was carried out to determine the protocol with the best metabolome coverage, efficiency and reproducibility. Solid/liquid extraction using the solvent mixture acetonitrile/methanol (50/50) was evaluated as the best protocol. Microbial diversity in lagoon sediment was also measured after DNA extraction using five commercial extraction kits. Our study showed that the DNeasy PowerSoil Pro Qiagen kit (Promega, USA) was the most suitable for assessing microbial diversity in fresh sediment.

The impact of DNA extraction on the quantification of Legionella, with implications for ecological studies

Monitoring the levels of opportunistic pathogens in drinking water is important to plan interventions and understand the ecological niches that allow them to proliferate. Quantitative PCR is an established alternative to culture methods that can provide a faster, higher-throughput, and more precise enumeration of the bacteria in water samples. However, PCR-based methods are still not routinely applied for Legionella monitoring, and techniques, such as DNA extraction, differ notably between laboratories. Here, we quantify the impact that DNA extraction methods had on downstream PCR quantification and community sequencing. Through a community science campaign, we collected 50 water samples and corresponding shower hoses, and compared two commonly used DNA extraction methodologies to the same biofilm and water phase samples. The two methods showed clearly different extraction efficacies, which were reflected in both the quantity of DNA extracted and the concentrations of Legionella enumerated in both the matrices. Notably, one method resulted in higher enumeration in nearly all samples by about one order of magnitude and detected Legionella in 21 samples that remained undetected by the other method. 16S rRNA amplicon sequencing revealed that the relative abundance of individual taxa, including sequence variants of Legionella, significantly varied depending on the extraction method employed. Given the implications of these findings, we advocate for improvement in documentation of the performance of DNA extraction methods used in drinking water to detect and quantify Legionella, and characterize the associated microbial community.IMPORTANCEMonitoring for the presence of the waterborne opportunistic pathogen Legionella is important to assess the risk of infection and plan remediation actions. While monitoring is traditionally carried on through cultivation, there is an ever-increasing demand for rapid and high-throughput molecular-based approaches for Legionella detection. This paper provides valuable insights on how DNA extraction affects downstream molecular analysis such as the quantification of Legionella through droplet digital PCR and the characterization of natural microbial communities through sequencing analysis. We analyze the results from a risk-assessment, legislative, and ecological perspective, showing how initial DNA processing is an important step to take into account when shifting to molecular-based routine monitoring and discuss the central role of consistent and detailed reporting of the methods used.

Comparative analysis of endophyte diversity of Dendrobium officinale lived on rock and tree

Dendrobium officinale usually lives on rock or tree, but their endophyte diversity has not yet been fully revealed? In this study, high-throughput sequencing technology was used to investigate the endophyte diversity of the roots of D. officinale lived on tree (Group 1-3, arboreal type) and rock (Group 4, lithophytic type). The results showed that their composition of endophytic fungi and bacteria were similar at phylum level, while their relative abundance were different. Their taxa composition and abundance of endophytes differed significantly among groups at the genus level. Alpha diversity of endophytic fungi of lithophytic type was higher than those from arboreal type, while there was no advantage in endophytic bacteria. Beta diversity revealed that the endophytic fungi tended to cluster in each group, but the endophytic bacteria were dispersed among the groups. LEfSe analysis found that the numbers of predicted endophyte biomarkers of lithophytic type were more than arboreal types at genus level, and the biomarkers varied among groups. Microbial network analysis revealed similarities and differences in the taxa composition and abundance of shared and special endophytes in each group. These results suggested that the root endophytes of lithophytic and arboreal D. officinale differed in diversity.

Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau

BACKGROUND

The microbial biodiversity and the role of microorganisms in the fermentation of washed coffee in Colombia were investigated using the Bourbon and Castillo coffee varieties. DNA sequencing was used to evaluate the soil microbial biota and their contribution to fermentation. The potential benefits of these microorganisms were analyzed, including increased productivity and the need to understand the rhizospheric bacterial species to optimize these benefits.

METHODS

This study used coffee beans for DNA extraction and 16 S rRNA sequencing. The beans were pulped, samples were stored at 4ºC, and the fermentation process was at 19.5ºC and 24ºC. The fermented mucilage and root-soil samples were collected in duplicate at 0, 12, and 24 h. DNA was extracted from the samples at a concentration of 20 ng/µl per sample, and the data obtained were analyzed using the Mothur platform.

RESULTS

The study demonstrates that the coffee rhizosphere is a diverse ecosystem composed primarily of microorganisms that cannot be cultured in the laboratory. This suggests that the microbial community may vary depending on the coffee variety and play an essential role in fermentation and overall coffee quality.

CONCLUSIONS

The study highlights the importance of understanding and optimizing the microbial diversity in coffee production, which could have implications for the sustainability and success of coffee production. DNA sequencing techniques can help characterize the structure of the soil microbial biota and evaluate its contribution to coffee fermentation. Finally, further research is needed to fully understand the biodiversity of coffee rhizospheric bacteria and their role.

Optimized Sample Processing Pipeline for PCR-Based Fungicide Resistance Quantification of Stubble-Borne Fungal Pathogens

Globally, yield losses associated with failed crop protection due to fungicide-resistant pathogens present an increasing problem. For stubble-borne pathogens, assessment of crop residues during the off-season could provide early fungicide resistance quantification for informed management decisions to mitigate yield losses. However, stubble assessment is hampered by assay inhibitors that are derived from decaying organic matter. To overcome assay inhibition from weathered stubble samples, we used a systems approach to quantify the frequency of resistance to demethylase inhibitor fungicides of the barley pathogen Pyrenophora teres f. teres. The system canvassed (i) 10 ball-milling conditions; (ii) four DNA extraction methodologies; and (iii) three column purification techniques for the provision of sufficient yield, quality, and purity of fungal DNA for a PCR-based fungicide resistance assay. Results show that DNA quantity and purity differed within each of the above three categories, with the optimized pipeline being (i) ball-milling samples in a 50-ml stainless steel canister for 5 min using a 20-mm ball at 30 revolutions s^-1; (ii) a modified Brandfass method (extracted 64% more DNA than other methods assessed); and (iii) use of silica resin columns for the highest DNA concentration with optimal DNA purity. The chip-digital PCR assay, which quantified fungicide resistance from field samples, was unaffected by the DNA extraction method or purification technique, provided that thresholds of template quantity and purity were satisfied. In summary, this study has developed molecular pipeline options for pathogen fungicide resistance quantification from cereal stubbles, which can guide management for improved crop protection outcomes.

Recovery of the soil fungal microbiome after steam disinfection to manage the plant pathogen Fusarium solani

Soil disinfection using high temperatures via steam is a promising approach to manage plant pathogens, pests, and weeds. Soil steaming is a viable option for growers who are moving away from dependence on chemical soil fumigants, especially in plant nursery or high tunnel environments. However, there are few studies that investigate how soil steaming causes substantial disturbance to the soil by killing both target pathogens and other soil biota. Steaming treatments also change the trajectory of the soil microbiome as it reassembles over time. Growers are interested in the health of soils after using steam-disinfection, especially if a virulent pathogen colonizes the soil and then flourishes in a situation where there are very few microbes to suppress its growth. Should recruitment of a virulent pathogen occur in the soil, this could have devasting effects on seed germination, seedling establishment and survival. Beneficial microbes are often used to prevent the colonization of plant pathogens, especially after a soil-steaming event. Here, we experimentally test how soil fungal communities assemble after steaming disinfection. We introduce to steam-treated soil Fusarium solani, an important fungal pathogen of soybean and Trichoderma harzianum, a known beneficial fungus used for soilborne pathogen suppression. Results show that F. solani significantly affects the relative abundance and diversity of the soil fungal microbiome, however, T. harzianum does not mitigate the amount of F. solani in the steam treated soil. Within the T. harzianum microbial addition, the soil fungal communities were similar to the control (steaming only). This result suggests inoculating the soil with T. harzianum does not drastically alter the assembly trajectory of the soil fungal microbiome. Other soil amendments such as a combination of Trichoderma spp. or other genera could suppress F. solani growth and shift soil microbiome composition and function post-steaming, however, more experimental research is needed.

Does plastic type matter? Insights into non-indigenous marine larvae recruitment under controlled conditions

Marine plastic debris (MPD) are a global threat to marine ecosystems. Among countless ecosystem impacts, MPD can serve as a vector for marine 'hitchhikers' by facilitating transport and subsequent spread of unwanted pests and pathogens. The transport and spread of these non-indigenous species (NIS) can have substantial impacts on native biodiversity, ecosystem services/functions and hence, important economic consequences. Over the past decade, increasing research interest has been directed towards the characterization of biological communities colonizing plastic debris, the so called Plastisphere. Despite remarkable advances in this field, little is known regarding the recruitment patterns of NIS larvae and propagules on MPD, and the factors influencing these patterns. To address this knowledge gap, we used custom-made bioassay chambers and ran four consecutive bioassays to compare the settlement patterns of four distinct model biofouling organisms' larvae, including the three notorious invaders Crassostrea gigas, Ciona savignyi and Mytilus galloprovincialis, along with one sessile macro-invertebrate Spirobranchus cariniferus, on three different types of polymers, namely Low-Linear Density Polyethylene (LLDPE), Polylactic Acid (PLA), Nylon-6, and a glass control. Control bioassay chambers were included to investigate the microbial community composition colonizing the different substrates using 16S rRNA metabarcoding. We observed species-specific settlement patterns, with larvae aggregating on different locations on the substrates. Furthermore, our results revealed that C. savignyi and S. cariniferus generally favoured Nylon and PLA, whereas no specific preferences were observed for C. gigas and M. galloprovincialis. We did not detect significant differences in bacterial community composition between the tested substrates. Taken together, our results highlight the complexity of interactions between NIS larvae and plastic polymers. We conclude that several factors and their potential interactions influenced the results of this investigation, including: (i) species-specific larval biological traits and ecology; (ii) physical and chemical composition of the substrates; and (iii) biological cues emitted by bacterial biofilm and the level of chemosensitivity of the different NIS larvae. To mitigate the biosecurity risks associated with drifting plastic debris, additional research effort is critical to effectively decipher the mechanisms involved in the recruitment of NIS on MPD.

Environmental DNA-based profiling of benthic bacterial and eukaryote communities along a crude oil spill gradient in a coral reef in the Persian Gulf

Coral reef ecosystems in the Persian Gulf are frequently exposed to crude oil spills. We investigated benthic bacterial and eukaryote community structures at such coral reef sites subjected to different degrees of polycyclic aromatic hydrocarbon (PAH) pollution using environmental DNA (eDNA) metabarcoding. Both bacterial and eukaryote communities responded with pronounced shifts to crude oil pollution and distinguished control sites, moderately and heavily impacted sites with significant confidentiality. The observed community patterns were predominantly driven by Alphaproteobacteria and metazoans. Among these, we identified individual genera that were previously linked to oil spill stress, but also taxa, for which a link to hydrocarbon still remains to be established. Considering the lack of an early-warning system for the environmental status of coral reef ecosystems exposed to frequent crude-oil spills, our results encourage further research towards the development of an eDNA-based biomonitoring tool that exploits benthic bacterial and eukaryote communities as bioindicators.

Application of MinION sequencing as a tool for the rapid detection and characterization of Listeria monocytogenes in smoked salmon

Microbial pathogens may be present in different types of foods, and hence the development of novel methods to assure consumers' safeness is of great interest. Molecular methods are known to provide sensitive and rapid results; however, they are typically targeted approaches. In recent years, the advent of non-targeted approaches based on next-generation sequencing (NGS) has emerged as a rational way to proceed. This technology allows for the detection of several pathogens simultaneously. Furthermore, with the same set of data, it is possible to characterize the microorganisms in terms of serotype, virulence, and/ or resistance genes, among other molecular features. In the current study, a novel method for the detection of Listeria monocytogenes based on the "quasimetagenomics" approach was developed. Different enrichment media and immunomagnetic separation (IMS) strategies were compared to determine the best approach in terms of L. monocytogenes sequences generated from smoked salmon samples. Finally, the data generated were analyzed with a user-friendly workflow that simultaneously provided the species identification, serotype, and antimicrobial resistance genes. The new method was thoroughly evaluated against a culture-based approach, using smoked salmon inoculated with L. monocytogenes as the matrix of choice. The sequencing method reached a very low limit of detection (LOD50, 1.2 CFU/ 25 g) along with high diagnostic sensitivity and specificity (100%), and a perfect correlation with the culture-based method (Cohen's k = 1.00). Overall, the proposed method overcomes all the major limitations reported for the implementation of NGS as a routine food testing technology and paves the way for future developments taking its advantage into consideration.

Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition

The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470-490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342-3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.

Seasonal phytoplankton and geochemical shifts in the subsurface chlorophyll maximum layer of a dimictic ferruginous lake

Subsurface chlorophyll maxima layers (SCML) are ubiquitous features of stratified aquatic systems. Availability of the micronutrient iron is known to influence marine SCML, but iron has not been explored in detail as a factor in the development of freshwater SCML. This study investigates the relationship between dissolved iron and the SCML within the dimictic, ferruginous lake Grosses Heiliges Meer in northern Germany. The occurrence of the SCML under nonferruginous conditions in the spring and ferruginous conditions in the fall are context to explore temporal changes in the phytoplankton community and indicators of primary productivity. Results indicate that despite more abundant chlorophyll in the spring, the SCML sits below a likely primary productivity maximum within the epilimnion, inferred based on colocated dissolved oxygen, δ13 CDIC , and pH maxima. The peak amount of chlorophyll in the SCML is lower in the fall than in the spring, but in the fall the SCML is colocated with elevated dissolved iron concentrations and a local δ13 CDIC maximum. Cyanobacteria and Chlorophyta have elevated abundances within the SCML in the fall. Further investigation of the relationship of iron to primary productivity within ferruginous SCML may help to understand the environmental controls on primary productivity in past ferruginous oceans.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

Aquaculture production of hatchling Hawaiian Bobtail Squid (Euprymna scolopes) is negatively impacted by decreasing environmental microbiome diversity

Aims

The Hawaiian Bobtail Squid (Euprymna scolopes) is a model organism for investigating host–symbiont relationships. The current scientific focus is on the microbiome within E. scolopes, while very little is known about the microbiome of the tanks housing E. scolopes. We examined the hypothesis that bacterial communities and geochemistry within the squid tank environment correlate with the production of viable paralarval squid.

Methods and Results

Total DNA was extracted from sediment and filtered water samples from ‘productive’ squid cohorts with high embryonic survival and paralarval hatching, ‘unproductive’ cohorts with low embryonic survival and paralarval hatching. As a control total DNA was extracted from environmental marine locations where E. scolopes is indigenous. Comparative analysis of the bacterial communities by the 16S rRNA gene was performed using next generation sequencing. Thirty‐eight differentially abundant genera were identified in the adult tank waters. The majority of the sequences represented unclassified, candidate or novel genera. The characterized genera included Aquicella, Woeseia and Ferruginibacter, with Hyphomicrobium and Rhizohapis were found to be more abundant in productive adult tank water. In addition, nitrate and pH covaried with productive cohorts, explaining 67% of the bacterial populations. The lower abundance of nitrate‐reducing bacteria in unproductive adult tank water could explain detected elevated nitrate levels.

Conclusions

We conclude that microbiome composition and water geochemistry can negatively affect E. scolopes reproductive physiology in closed tank systems, ultimately impacting host‐microbe research using these animals.

Significance and Impact of study

These results identify the tight relationship between the microbiome and geochemistry to E. scolopes. From this study, it may be possible to design probiotic counter‐measures to improve aquaculture conditions for E. scolopes.

Microbial community succession on submerged vertebrate carcasses in a tidal river habitat: Implications for aquatic forensic investigations

Death investigations in aquatic ecosystems are challenging due to abiotic and biotic factors that may influence the estimation of a postmortem submersion interval (PMSI). In this study, we examined bacterial changes throughout the decomposition process on porcine carcasses submerged in a tidal-influenced river and identified predictors of epinecrotic community succession. Fetal porcine (Sus scrofa) carcasses (N = 6) were submerged with epinecrotic samples collected every 3 days (6 collections) over a period of 19 days (~7415 accumulated degree hours (ADH)). Amplicon sequencing was performed using the Illumina MiSeq platform (16S V4 region, 2 × 250 bp format) to identify changes in bacterial relative abundance and diversity. To match bacterial succession with rough taphonomy, carcasses were visually assessed at each sampling time point to determine the decomposition stage. Notably, the three most abundant families were Moraxellaceae, Burkholderiaceae (Proteobacteria), and Clostridiaceae (Firmicutes), though communities composition varied significantly across decomposition stages. Greater bacterial phylogenetic diversity was observed in in latter decomposition stages (advanced floating decay, sunken remains). Random Forest Models were built to predict ADH and explained 77%-80.8% of variation in ADH with an error rate of +/-1943.2 ADH (Root Mean Square Error) or approx. ±2.7 days at the mean water temperature of this study. This study provided a useful model that could be used to estimate a PMSI in this river system utilizing bacterial community succession, and thus, potentially improve the accuracy of such estimations to be used in the court of law.

Grab what you can-an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding

Environmental DNA methods such as metabarcoding have been suggested as possible alternatives or complements to the current practice of morphology-based diversity assessment for characterizing benthic communities in marine sediment. However, the source volume used in sediment eDNA studies is several magnitudes lower than that used in morphological identification. Here, we used data from a North Sea benthic sampling station to investigate to what extent metabarcoding data is affected by sampling bias and spatial heterogeneity. Using three grab parallels, we sampled five separate sediment samples from each grab. We then made five DNA extraction replicates from each sediment sample. Each extract was amplified targeting both the 18S SSU rRNA V1–V2 region for total eukaryotic composition, and the cytochrome c oxidase subunit I (COI) gene for metazoans only. In both datasets, extract replicates from the same sediment sample were significantly more similar than different samples from the same grab. Further, samples from different grabs were less similar than those from the same grab for 18S. Interestingly, this was not true for COI metabarcoding, where the differences within the same grab were similar to the differences between grabs. We also investigated how much of the total identified richness could be covered by extract replicates, individual sediment samples and all sediment samples from a single grab, as well as the variability of Shannon diversity and, for COI, macrofaunal biotic indices indicating environmental status. These results were largely consistent with the beta diversity findings, and show that total eukaryotic diversity can be well represented using 18S metabarcoding with a manageable number of biological replicates. Based on these results, we strongly recommend the combination of different parts of the surface of single grabs for eDNA extraction as well as several grab replicates, or alternatively box cores or similar. This will dilute the effects of dominating species and increase the coverage of alpha diversity. COI-based metabarcoding consistency was found to be lower compared to 18S, but COI macrofauna-based indices were more consistent than direct COI alpha diversity measures.

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores

Lake sediments are natural archives that accumulate information on biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further research investigating factors such as sample heterogeneity and DNA degradation are required. In the present study we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices (1-cm width). Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each depth slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Accumulation curves demonstrated that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each depth slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Replicates within a depth slice generally clustered together in the Non-metric multidimensional scaling analysis. There was high community dissimilarity in older sediment in one of the cores, which was likely due to the laminae in the sediment core not being horizontal. Given that most paleolimnology studies explore broad scale shifts in community structure rather than seeking to identify rare species, this study demonstrates that a single sample is adequate to characterise shifts in dominant bacterial ASVs.

Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance

The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and deposition processes, hydrochemistry and pH, and contaminating agents. These approaches must also provide a robust framework that meets the need for biosecurity management decisions regarding threats to human health, environmental resources, and economic interests, especially in areas with limited clean-laboratory resources and experienced personnel. This contribution aims to facilitate dialogue and innovation within this sector by reviewing current approaches for sample collection, post-sampling capture and concentration of eDNA, preservation, and extraction, all through a biosecurity monitoring lens.