Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans.

Bermuda is an isolated 5560 ha chain of limestone islands on a 150 000 ha seamount located near 32°N, 64°W. Meadows of tropical and subtropical seagrasses, dominated by Thalassia testudinum and Syringodium filiforme, are found from inshore bays out to the inner edge of the rim reef that encircles the platform. Fine-scale computerized mapping and subsequent broad-scaled field assessment of seagrass meadows in Bermuda show that (1) meadows representing nearly one-quarter of the territory's total seagrass area in 1997 had declined by 2004, (2) net loss of seagrass meadows occurred at rim reef and lagoonal locations that are far-removed from anthropogenic disturbances, (3) the decline appears to have been in progress as early as 1996, and (4) both T. testudinum and S. filiforme meadows declined. Nearly 2100 ha of meadows were visible in a 1997 georeferenced mosaic of aerial photographs of the Bermuda platform. In 2004, 22 meadows that represented about 475 of the 900 ha of offshore seagrass identified in 1997 and earlier were absent or in obvious decline. The size and location of inshore and nearshore meadows, which are exposed to intense anthropogenic stresses and physical damage, varied over the same 7 yr but their total area has either remained unchanged or even increased. Processes contributing to the decline in offshore meadows have yet to be determined, but may include herbivory by juvenile green turtles and parrotfishes and below-normal productivity owing to a winter cold-water event correlated with a change in the North Atlantic Oscillation (NAO) in 1996. The potential consequences to Bermuda of the loss of nearly 500 ha of critical marine habitat are of extreme concern.

Global trade by merchant ships is a leading mechanism for the unintentional transfer of marine organisms, including non-indigenous species, to bays and estuaries worldwide. To reduce the likelihood of new invasions, ships are increasingly being required to manage their ballast water (BW) prior to discharge in coastal waters. In the United States, most overseas arrivals have been required to manage BW discharge since 2004, primarily through ballast water exchange (BWE), which flushes out ballast tanks in the open ocean (>200 miles from shore). Studies have found BWE to generally reduce the abundance of organisms, and the amount of water exchanged has been estimated at 96–100%. Despite its widespread use, the overall effect of this management strategy on net propagule supply through time has not been explored. Here, temporal changes in zooplankton concentrations and the volume of BW discharged in Chesapeake Bay, U.S. were evaluated, comparing pre-management era and post-management era time periods. Chesapeake Bay is a large port system that receives extensive BW discharge, especially from bulk cargo vessels (bulkers) that export coal overseas. For bulkers arriving from overseas, mean zooplankton concentrations of total and coastal indicator taxa in BW did not decline between pre- (1993–2000) and post management (2012–2013) eras, when controlling for season and sampling method. Moreover, bulkers discharged 21 million tonnes (82% of total for Chesapeake Bay) of overseas BW in 2013, representing a 374% increase in volume when compared to 2005. The combination of BW discharge volume and zooplankton concentration data indicates that (a) net propagule supply by bulkers has increased since BWE began in Chesapeake Bay; and (b) changes in vessel behaviour and trade have contributed strongly to this outcome. Specifically, the coal-driven increase in BW discharge volume from 2005–2013, concurrent with the onset of BWE regulations, worked to counteract intended results from BW management. A long-term analysis of bulker arrivals (1994–2013) reveals a 20-year minimum in arrival numbers in 2000, just when the implementation of BWE began. This study underscores the need to consider shifts in trade patterns, in order to advance and evaluate effective management strategies for biological invasions.

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