Nucleic acids-based tools for ballast water surveillance, monitoring, and research

Fast and sensitive detection of viable Escherichia coli O157:H7 using a microwell-confined and propidium monoazide-assisted digital CRISPR microfluidic platform

Escherichia coli O157:H7 is a major foodborne pathogen that poses a significant threat to food safety and human health. Rapid and sensitive detection of viable Escherichia coli O157:H7 can effectively prevent food poisoning. Here, we developed a microwell-confined and propidium monoazide-assisted digital CRISPR microfluidic platform for rapid and sensitive detection of viable Escherichia coli O157:H7 in food samples. The reaction time is significantly reduced by minimizing the microwell volume, yielding qualitative results in 5 min and absolute quantitative results in 15 min. With the assistance of propidium monoazide, this platform can eliminate the interference from 99% of dead Escherichia coli O157:H7. The direct lysis method obviates the need for a complex nucleic acid extraction process, offering a limit of detection of 3.6 × 101 CFU mL-1 within 30 min. Our results demonstrated that the platform provides a powerful tool for rapid detection of Escherichia coli O157:H7 and provides reliable guidance for food safety testing.

Bacterial communities in ballast tanks of cargo vessels - Shaped by salinity, treatment and the point of origin of the water but "hatch" its typical microbiome

Ballast water is a main vector of introduction of potentially harmful or pathogenic aquatic organisms. The development of genetic tools for ballast water monitoring has been underway and highlighted as a source for accurate and reliable data for decision making. We used 16S rRNA gene amplicon sequencing to analyze the microbial communities found in the ballast water of fifteen commercial ships routed through two Estonian ports. In parallel, samples from the port area were collected at the same time each ship visited. Fluorescence microscopy was utilized to assess the effectiveness of the treatment applied to ballast water. In addition, supplemental samples were collected from Hamburg Port (Germany) and a ballast tank decontamination system used at this port. The composition and diversity of bacterial communities varied greatly between obtained samples. The application of UV treatment did not demonstrate significant reduction in species richness estimates. The composition of microbial communities was significantly influenced by salinity, treatment (mainly untreated or UV treated) and the point of origin of the ballast water. Over a hundred potentially pathogenic bacterial taxa were found in relatively high abundance, including in ballast water that had received UV treatment. These shortcomings of stand-alone UV treatment of ballast water, especially when weak treatment is applied insufficiently, highlight the danger of possible harmful effects arising over time and the need for genetic tools for ballast water monitoring and management.

First evaluation of ballast water management systems on operational ships for minimizing introductions of nonindigenous zooplankton

Ballast water is a leading pathway for the global introduction of aquatic nonindigenous species. Most international ships are expected to install ballast water management systems (BWMS) by 2024 to treat ballast water before release. This study examines if ballast water discharges managed by BWMS are meeting standards for organisms ≥50 μm in minimum dimension (i.e., <10 organisms per m3; typically zooplankton). Representative samples of ballast water were collected from 29 ships (using 14 different BWMS) arriving to Canada during 2017-2018. Fourteen samples (48 %) had zooplankton concentrations clearly exceeding the standard (ranging from 18 to 3822 organisms per m3). Nonetheless, compared to earlier management strategies, BWMS appear to reduce the frequency of high-risk introduction events. BWMS filter mesh size was an important predictor of zooplankton concentration following treatment. Greater rates of compliance may be achieved as ship crews gain experience with operation and maintenance of BWMS.

International shipping as a potent vector for spreading marine parasites

Aim

The global shipping fleet, the primary means of transporting goods among countries, also serves as a major dispersal mechanism for marine invasive species. To date, researchers have primarily focussed on the role of ships in transferring marine macrofauna, often overlooking transfers of associated parasites, which can have larger impacts on naïve host individuals and populations. Here, we re-examine three previously published metabarcode datasets targeting zooplankton and protists in ships' ballast water to assess the diversity of parasites across life stages arriving to three major US ports.

Location

Port of Hampton Roads in the Chesapeake Bay, Virginia; Ports of Texas City, Houston and Bayport in Galveston Bay, Texas; and Port of Valdez in Prince William Sound, Alaska.

Methods

We selected all known parasitic taxa, using sequences generated from the small subunit gene (SSU) from ribosomal RNA (rRNA) amplified from (1) zooplankton collected from plankton tows (35 and 80 μm datasets) and (2) eukaryotes collected from samples of ships' ballast water (3 μm dataset).

Results

In all three datasets, we found a broad range of parasitic taxa, including many protistan and metazoan parasites, that infect a wide range of hosts, from teleost fish to dinoflagellates. Parasite richness was highest in the 3 μm dataset and relatively uniform across arrival regions. Several parasite taxa were found in high relative abundance (based on number of sequences recovered) either in ships entering a single or across multiple regions.

Main Conclusions

The ubiquity, diversity and relative abundance of parasites detected demonstrate ships are a potent vector for spreading marine parasites across the world's oceans, potentially contributing to reported increases in outbreaks of marine diseases. Future research is urgently needed to evaluate the fate of parasites upon arrival and the efficacy of ballast water treatment systems to reduce future transfers and colonization.

Measuring viability of dinoflagellate cysts and diatoms with stains to test the efficiency of facsimile treatments possibly applicable to ships' ballast water and sediment

Expansion of harmful algal bloom (HAB) species through ships' ballast water and sediment has been an increasing concern. Determining whether a microalgal cell, particularly for the toxic and HAB-forming species, is "viable" or "dead" is fundamental to understanding the effectiveness of the many ballast-water treatments that have been considered. To this end, we screened a variety of stains to assess the viability of dinoflagellate (Gymnodinium catenatum, GC) cysts and diatom (Corethron hystrix) vegetative cells to test the efficiency of ballast water treatments. Results showed that the stains fluorescing red or green are not sound candidates for viability measurements due to the interference of chlorophyll-induced red fluorescence or cytosolic green autofluorescence, while the use of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide is limited by its toxicity, pseudo-positive judgment and the consequent confusion between cysts and vegetative cells. We further demonstrated that the stain Neutral Red (NR) is a sound candidate as the "vital stain" and can be easily applied for functionally defining the viability of both dinoflagellate cysts and diatoms. Another stain, the Evans Blue (EB), could be used as a "mortal stain" for the vegetative diatom cells but not a sensitive indicator of viability for GC cysts. The NR staining for GC cysts generally needs a higher dosage (0.005%) and longer staining time (24 h) than that were used for staining zooplankton, diatoms, and vegetative cells of dinoflagellates. In all cases, EB staining defined a "percentage of viable cells" significantly higher than that defined by NR. We conclude that the viability of a population is highly dependent on the species of stains used thus must be referred as a method-defined indicator.

Bacterial diversity in ballast water and sediments revealed by 2b-RAD sequencing

Despite that the ballast water management (BWM) convention has come into force to prevent the spread of harmful aquatic organisms, to date, very few bacteria can be identified through microbial culture method. In this study, we explored a reduced-representation sequencing of 2b-RAD approach to investigate the bacterial diversity in ballast water and sediments (BWS). Our results indicated a large amount of bacteria species (1496) detected in BWS up to now, including 13 pathogens that are seriously concerning in marine environment and aquaculture like the most harmful Vibrio harveyi and Aurantimonas coralicida. We showed that the ballast water had relative lower species, which was dominated by Proteobacteria. In contrast, the sediments had richer species, which was dominated by Bacteroidetes. Although BWS differed significantly in species composition, sediments shared most of the concerned pathogens with ballast water, highlighting the importance of sediment management. In conclusion, 2b-RAD sequencing shows promise in future BWM.

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. DNA extraction kits have been widely used and the 18S rRNA and the COI genes the most employed markers, but less than half of the studies targeted more than one marker loci. The Illumina MiSeq platform has been used in >50% of the publications. Current weaknesses include potential occurrence of false negatives due to the primer-biased or faulty DNA amplification and the incompleteness of reference libraries. This is particularly concerning in the case of NIS surveillance, where proficiency in species level detection is critical. Until these weaknesses are resolved, ideally NIS metabarcoding should be supported by complementary approaches, such as morphological analysis or more targeted molecular approaches (e.g. qPCR, ddPCR). Even so, metabarcoding has already proved to be a highly sensitive tool to detect small organisms or undifferentiated life stages across a wide taxonomic range. In addition, it also seems to be very effective in ballast water management and to improve the spatial and temporal sampling frequency of NIS surveillance in marine and coastal ecosystems. Although specific protocols may be required for species-specific NIS detection, for general monitoring it would be vital to settle on a standard protocol able to generate comparable results among surveillance campaigns and regions of the globe, seeking the best approach for detecting the broadest range of species, while minimizing the chances of a false positive or negative detection.

Metabarcoding quantifies differences in accumulation of ballast water borne biodiversity among three port systems in the United States

Characterizing biodiversity conveyed in ships' ballast water (BW), a global driver of biological invasions, is critically important for understanding risks posed by this key vector and establishing baselines to evaluate changes associated with BW management. Here we employ high throughput sequence (HTS) metabarcoding of the 18S small subunit rRNA to test for and quantify differences in the accumulation of BW-borne biodiversity among three distinct recipient port systems in the United States. These systems were located on three different coasts (Pacific, Gulf, and Atlantic) and chosen to reflect distinct trade patterns and source port biogeography. Extensive sampling of BW tanks (n = 116) allowed detailed exploration of molecular diversity accumulation. Our results indicate that saturation of introduced zooplankton diversity may be achieved quickly, with fewer than 25 tanks needed to achieve 95% of the total extrapolated diversity, if source biogeography is relatively limited. However, as predicted, port systems with much broader source geographies require more extensive sampling to estimate diversity, which continues to accumulate after sampling >100 discharges. The ability to identify BW sources using molecular indicators was also found to depend on the breadth of source biogeography and the extent to which sources had been sampled. These findings have implications both for the effort required to fully understand introduced diversity and for projecting risks associated with future changes to maritime traffic that may increase source biogeography for many recipient ports. Our data also suggest that molecular diversity may not decline significantly with BW age, indicating either that some organisms survive longer than recognized in previous studies or that nucleic acids from dead organisms persist in BW tanks. We present evidence for detection of potentially invasive species in arriving BW but discuss important caveats that preclude strong inferences regarding the presence of living representatives of these species in BW tanks.

Elucidating Biodiversity Shifts in Ballast Water Tanks during a Cross-Latitudinal Transfer: Complementary Insights from Molecular Analyses

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.

Genomic and Microscopic Analysis of Ballast Water in the Great Lakes Region

Invasive aquatic species can have damaging effects on fisheries and aquaculture through significant, and irreversible, effects on biodiversity. Human health may also be affected. To combat this threat the International Maritime Organization (IMO) Convention for Ballast Water and Sediments (BWMC) came into force in September 2017. U.S. Federal and IMO ballast water standards for discharged organisms stipulate discharge limits for different size classes of organisms. Several studies including recent trials aboard Great Lakes freighters have shown that many phytoplankton found in ballast water do not fall into the regulated 10–50 µM size class. Such issues illustrate the need for new methods of assessing microorganism populations that will supersede laborious microscopy requiring rare technical expertise. Recent progress has been made in the use of DNA (deoxyribose nucleic acid)-based methods as a means of identifying the appearance of invasive species in aquatic environments. A significant advance has been the development of high throughput sequencing (HTS), which has expanded DNA barcoding, relating to an individual organism, into second generation sequencing (metabarcoding), capable of mapping whole populations of organisms in an environmental sample. Several recent studies of HTS in ships’ ballast water, have shown that the technique has the capacity for detecting potentially harmful taxonomic groups and is capable of differentiating among water from different sources. The current study was undertaken to investigate the suitability (or otherwise) of HTS as a tool for ballast water management. Possible applications include improved risk assessment relating to invasive species. Feasibility for indicative testing for ballast water treatment efficacy was also addressed. However, pending analysis of treated samples, the current study was confined to a comparison of HTS and microscope counts in untreated samples. A correlation of visual and molecular taxonomic assignments of microorganisms found in the ballast water from different ports and during different seasons indicated that such a comparison was best conducted at Family level, although Principal Components Analysis showed that the two methods differed qualitatively among major taxonomic groups.

Climate change opens new frontiers for marine species in the Arctic: Current trends and future invasion risks

Climate change and increased anthropogenic activities are expected to elevate the potential of introducing nonindigenous species (NIS) into the Arctic. Yet, the knowledge base needed to identify gaps and priorities for NIS research and management is limited. Here, we reviewed primary introduction events to each ecoregion of the marine Arctic realm to identify temporal and spatial patterns, likely source regions of NIS, and the putative introduction pathways. We included 54 introduction events representing 34 unique NIS. The rate of NIS discovery ranged from zero to four species per year between 1960 and 2015. The Iceland Shelf had the greatest number of introduction events (n = 14), followed by the Barents Sea (n = 11), and the Norwegian Sea (n = 11). Sixteen of the 54 introduction records had no known origins. The majority of those with known source regions were attributed to the Northeast Atlantic and the Northwest Pacific, 19 and 14 records, respectively. Some introduction events were attributed to multiple possible pathways. For these introductions, vessels transferred the greatest number of aquatic NIS (39%) to the Arctic, followed by natural spread (30%) and aquaculture activities (25%). Similar trends were found for introductions attributed to a single pathway. The phyla Arthropoda and Ochrophyta had the highest number of recorded introduction events, with 19 and 12 records, respectively. Recommendations including vector management, horizon scanning, early detection, rapid response, and a pan-Arctic biodiversity inventory are considered in this paper. Our study provides a comprehensive record of primary introductions of NIS for marine environments in the circumpolar Arctic and identifies knowledge gaps and opportunities for NIS research and management. Ecosystems worldwide will face dramatic changes in the coming decades due to global change. Our findings contribute to the knowledge base needed to address two aspects of global change-invasive species and climate change.

Ballast Water Exchange and Invasion Risk Posed by Intracoastal Vessel Traffic: An Evaluation Using High Throughput Sequencing

Ballast water remains a potent vector of non-native aquatic species introductions, despite increased global efforts to reduce risk of ballast water mediated invasions. This is particularly true of intracoastal vessel traffic, whose characteristics may limit the feasibility and efficacy of management through ballast water exchange (BWE). Here we utilize high throughput sequencing (HTS) to assess biological communities associated with ballast water being delivered to Valdez, Alaska from multiple source ports along the Pacific Coast of the United States. Our analyses indicate that BWE has a significant but modest effect on ballast water assemblages. Although overall richness was not reduced with exchange, we detected losses of some common benthic coastal taxa (e.g., decapods, mollusks, bryozoans, cnidaria) and gains of open ocean taxa (e.g., certain copepods, diatoms, and dinoflagellates), including some potentially toxic species. HTS-based metabarcoding identified significantly differentiated biodiversity signatures from individual source ports; this signal persisted, though weakened, in vessels undergoing BWE, indicating incomplete faunal turnover associated with management. Our analysis also enabled identification of taxa that may be of particular concern if established in Alaskan waters. While these results reveal a clear effect of BWE on diversity in intracoastal transit, they also indicate continued introduction risk of non-native and harmful taxa.

The Biological Basis for Ballast Water Performance Standards: "Viable/Non-Viable" or "Live/Dead"?

The shipping industry is critical to international commerce; however, contemporary shipping practices involve uptake and discharge of ballast water, which introduces the potential for transfer of nonindigenous, invasive species among geographically distinct habitats. To counteract this hazard, regulations for ballast water management have been implemented by the International Maritime Organization (IMO) and by regulatory agencies such as the United States Coast Guard (USCG). IMO and USCG discharge standards are numerically identical, but involve different definitions of treatment end points, which are based on fundamentally different biological assays for quantification of ballast water treatment effectiveness. Available assays for quantification of the responses of organisms in the 10-50 μm size range include vital stains based on fluorescein diacetate (FDA), sometimes used in combination with 5-chloromethylfluorescein diacetate (CMFDA), observations of motility, and the most probable number dilution culture method (MPN). The mechanisms and implications of these assays are discussed relative to the Type Approval process, which quantitatively evaluates compliance with ballast water discharge standards (BWDSs) under controlled shipboard and land-based tests. For antimicrobial processes that accomplish treatment by preventing subsequent replication of the target species, the FDA/CMFDA and MPN methods can yield dramatically different results. An important example of a treatment process that is affected by the choice of assay is ultraviolet (UV) irradiation. Results of laboratory and field experiments have demonstrated UV-based technologies to be effective for accomplishing the objectives of ballast water treatment (inactivation of cellular reproduction), when the MPN assay is used as the basis for evaluation. The FDA, CMFDA, motility, and MPN methods are subject to well recognized sources of error; however, the MPN method is based on a response that is consistent with the objectives of ballast water management as well as the mechanism of action of UV-based inactivation. Complementary assays are available for use in compliance testing; however, the development of relevant indicative tests remains as a research priority. Historical lessons learned from applications of vital stains (and other indirect methods) for quantification of microbial responses to UV irradiation in other settings also support the use of assays that provide a direct measure of growth and reproduction, such as MPN. Collectively, these observations point to the use of MPN assays as the standard for type testing, especially when UV-based treatment is employed.

Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

High-throughput sequencing metabarcoding studies in marine biosecurity have largely focused on targeting environmental DNA (eDNA). DNA can persist extracellularly in the environment, making discrimination of living organisms difficult. In this study, bilge water samples (i.e., water accumulating on-board a vessel during transit) were collected from 15 small recreational and commercial vessels. eDNA and eRNA molecules were co-extracted and the V4 region of the 18S ribosomal RNA gene targeted for metabarcoding. In total, 62.7% of the Operational Taxonomic Units (OTUs) were identified at least once in the corresponding eDNA and eRNA reads, with 19.5% unique to eDNA and 17.7% to eRNA. There were substantial differences in diversity between molecular compartments; 57% of sequences from eDNA-only OTUs belonged to fungi, likely originating from legacy DNA. In contrast, there was a higher percentage of metazoan (50.2%) and ciliate (31.7%) sequences in the eRNA-only OTUs. Our data suggest that the presence of eRNA-only OTUs could be due to increased cellular activities of some rare taxa that were not identified in the eDNA datasets, unusually high numbers of rRNA transcripts in ciliates, and/or artefacts produced during the reverse transcriptase, PCR and sequencing steps. The proportions of eDNA/eRNA shared and unshared OTUs were highly heterogeneous within individual bilge water samples. Multiple factors including boat type and the activities performed on-board, such as washing of scientific equipment, may play a major role in contributing to this variability. For some marine biosecurity applications analysis, eDNA-only data may be sufficient, however there are an increasing number of instances where distinguishing the living portion of a community is essential. For these circumstances, we suggest only including OTUs that are present in both eDNA and eRNA data. OTUs found only in the eRNA data need to be interpreted with caution until further research provides conclusive evidence for their origin.