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In the South Atlantic Bight (SAB), responses of zooplankton communities to physical dynamics were evaluated monthly at two sites on the continental shelf offshore from Savannah, GA, USA, between December 2015 and December 2017. Zooplankton were collected in oblique net tows (202-μm). Samples were collected in two regions of the middle shelf: inner edge (Site 1: 25 m isobath, n = 22) and outer edge (Site 2: 40 m isobath, n = 21). Samples were also collected at a third site on the 40 m isobath, ~20 nm south of Site 2 in July and August 2016. Temperature, salinity and fluorescence data were recorded at each site. Overall, 57 taxa were identified with total abundances varying from 1 × 103 to 81 × 103 ind.m−3. Small copepods predominated; notably Paracalanus spp. The highest abundance was recorded in October 2016 at Site 1, following deep mixing induced by Hurricane Matthew. Interannual variability of zooplankton abundance was significant, with higher abundances in 2016 compared with 2017, reflecting higher river runoff in 2016. Samples from Site 3 yielded the largest Dolioletta gegenbauri bloom documented in the SAB. This 2-year time-series, for the first time, suggests that zooplankton communities on the SAB middle shelf region are significantly influenced by continental precipitation patterns.

Bloom‐forming gelatinous zooplankton occur circumglobally and significantly influence the structure of pelagic marine food webs and biogeochemical cycling through interactions with microbial communities. During bloom conditions especially, gelatinous zooplankton are keystone taxa that help determine the fate of primary production, nutrient remineralization, and carbon export. Using the pelagic tunicateDolioletta gegenbaurias a model system for gelatinous zooplankton, we carried out a laboratory‐based feeding experiment to investigate the potential ecosystem impacts of doliolid gut microbiomes and microbial communities associated with doliolid faecal pellets and the surrounding seawater. Metabarcoding targeting Bacteria and Archaea 16S rRNA genes/Archaea) and qPCR approaches were used to characterize microbiome assemblages. Comparison between sample types revealed distinct patterns in microbial diversity and biomass that were replicable across experiments. These observations support the hypothesis that through their presence and trophic activity, doliolids influence the structure of pelagic food webs and biogeochemical cycling in subtropical continental shelf systems where tunicate blooms are common. Bacteria associated with starved doliolids (representative of the resident gut microbiome) possessed distinct low‐biomass and low‐diversity microbial assemblages, suggesting that the doliolid microbiome is optimized to support a detrital trophic mode. Bacterial generaPseudoalteromomasandShimiawere the most abundant potential core microbiome taxa, similar to patterns observed in other marine invertebrates. Exploratory bioinformatic analyses of predicted functional genes suggest that doliolids, via their interactions with bacterial communities, may affect important biogeochemical processes including nitrogen, sulphur, and organic matter cycling.

The study of invasive species often focuses on regions of recent introduction rather than native habitats. Understanding an invasive species in its natural environment, however, can provide important insights regarding the long-term outcome of invasions. In this study we investigated the diet of the invasive spiny water flea, Bythotrephes longimanus, in two Austrian perialpine lakes, where it is native. The gut contents of wild-caught Bythotrephes individuals were estimated by quantitative polymerase chain reaction, targeting species-specific fragments of the barcoding region of the cytochrome c oxidase I gene of potential prey. The observed prey spectrum of Bythotrephes in the study lakes consisted primarily of Eudiaptomus gracilis and Diaphanosoma brachyurum. The Daphnia longispina complex, Leptodora kindtii and Mesocyclops leuckarti also contributed to the diet. Results indicate that Bythotrephes is a generalist feeder with a preference for epilimnetic prey.

Gelatinous zooplankton play a crucial role in pelagic marine food webs, however, due to methodological challenges and persistent misconceptions of their importance, the trophic role of gelatinous zooplankton remains poorly investigated. This is particularly true for small gelatinous zooplankton including the marine pelagic tunicate,Dolioletta gegenbauri.D. gegenbauriand other doliolid species occur persistently on wide subtropical shelves where they often produce massive blooms in association with shelf upwelling conditions. As efficient filter feeders and prodigious producers of relatively low‐density organic‐rich aggregates, doliolids are understood to contribute significantly to shelf production, pelagic ecology, and pelagic–benthic coupling. Utilizing molecular gut content analysis and stable isotope analysis approaches, the trophic interactions of doliolids were explored during bloom and non‐bloom conditions on the South Atlantic Bight continental shelf in the Western North Atlantic. Based on molecular gut content analysis, relative ingestion selectivity varied withD. gegenbaurilife stage. At all life stages, doliolids ingested a wide range of prey types and sizes, but exhibited selectivity for larger prey types including diatoms, ciliates, and metazoans. Experimental growth studies confirmed that metazoan prey were ingested, but indicated that they were not digested and assimilated. Stable isotopic composition (δ¹³C and δ¹⁵N) of wild‐caught doliolids, during bloom and non‐bloom conditions, were most consistent with a detrital‐supplemented diet. These observations suggest that the feeding ecology ofD. gegenbauriis more complex than previously reported, and have strong and unusual linkages to the microbial food web.

Gelatinous zooplankton play a crucial role in marine planktonic food webs. However, primarily due to methodological challenges, the in situ diet of zooplankton remains poorly investigated and little is known about their trophic interactions including feeding behaviour, prey selection and in situ feeding rates. This is particularly true for gelatinous zooplankton including the marine pelagic tunicate,Dolioletta gegenbauri. In this study, we applied an 18S rRNA amplicon metabarcoding approach to identify the diet of captive‐fed and wild‐caughtD. gegenbaurion the midcontinental shelf of the South Atlantic Bight, USA. Sequencing‐based approaches were complimented with targeted quantitative real‐time polymerase chain reaction (PCR) analyses. Captive‐fedD. gegenbaurigut content was dominated by pico‐, nano‐ and micro‐plankton including pico‐dinoflagellates (picozoa) and diatoms. These results suggested that diatoms were concentrated byD. gegenbaurirelative to their concentration in the water column. Analysis of wild‐caught doliolids by quantitative real‐time PCR utilizing a group‐specific diatom primer set confirmed that diatoms were concentrated byD. gegenbauri, particularly by the gonozooid life stage associated with actively developing blooms. Sequences derived from larger metazoans were frequently observed in wild‐caught animals but not in captive‐fed animals suggesting experimental bias associated with captive feeding. These studies revealed that the diet ofD. gegenbauriis considerably more diverse than previously described, that parasites are common in wild populations, and that prey quality, quantity and parasites are likely all important factors in regulating doliolid population dynamics in continental shelf environments.