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1. Characterization of Two Novel Toti-Like Viruses Co-infecting the Atlantic Blue Crab, Callinectes sapidus, in Its Northern Range of the United States

   https://doi.org/10.3389/fmicb.2022.855750  

   Zhao, Mingli ; Xu, Lan ; Bowers, Holly ; Schott, Eric J. ( March 2022 , Frontiers in Microbiology)

   The advancement of high throughput sequencing has greatly facilitated the exploration of viruses that infect marine hosts. For example, a number of putative virus genomes belonging to the Totiviridae family have been described in crustacean hosts. However, there has been no characterization of the most newly discovered putative viruses beyond description of their genomes. In this study, two novel double-stranded RNA (dsRNA) virus genomes were discovered in the Atlantic blue crab ( Callinectes sapidus ) and further investigated. Sequencing of both virus genomes revealed that they each encode RNA dependent RNA polymerase proteins (RdRps) with similarities to toti-like viruses. The viruses were tentatively named Callinectes sapidus toti-like virus 1 (CsTLV1) and Callinectes sapidus toti-like virus 2 (CsTLV2). Both genomes have typical elements required for −1 ribosomal frameshifting, which may induce the expression of an encoded ORF1–ORF2 (gag-pol) fusion protein. Phylogenetic analyses of CsTLV1 and CsTLV2 RdRp amino acid sequences suggested that they are members of two new genera in the family Totiviridae . The CsTLV1 and CsTLV2 genomes were detected in muscle, gill, and hepatopancreas of blue crabs by real-time reverse transcription quantitative PCR (RT-qPCR). The presence of ~40 nm totivirus-like viral particles in all three tissues was verified by transmissionmore »electron microscopy, and pathology associated with CsTLV1 and CsTLV2 infections were observed by histology. PCR assays showed the prevalence and geographic range of these viruses, to be restricted to the northeast United States sites sampled. The two virus genomes co-occurred in almost all cases, with the CsTLV2 genome being found on its own in 8.5% cases, and the CsTLV1 genome not yet found on its own. To our knowledge, this is the first report of toti-like viruses in C. sapidus . The information reported here provides the knowledge and tools to investigate transmission and potential pathogenicity of these viruses.« less
2. Blue crab Callinectes sapidus dietary habits and predation on juvenile winter flounder Pseudopleuronectes americanus in southern New England tidal rivers

   https://doi.org/10.3354/meps13909  

   Taylor, DL ; Fehon, MM ; Cribari, KJ ; Scro, AK ( January 2022 , Marine Ecology Progress Series)

   Blue crabs Callinectes sapidus have expanded their geographic range northward in the NW Atlantic with possible trophodynamic effects on benthic communities. In this study, we examined the blue crab’s diet in 2 southern New England tidal rivers (USA) and expounded on their predator-prey interaction with juvenile winter flounder Pseudopleuronectes americanus . Blue crabs (8-185 mm carapace width [CW]; n = 1835) were collected from the Seekonk River, Rhode Island, and Taunton River, Massachusetts, between May and August 2012 to 2016, and their feeding habits were assessed via stomach content, stable isotope, and molecular genetic analyses. Blue crabs were found to be generalist carnivores-omnivores with diets varying throughout ontogeny, yet shifts in prey composition had no effect on size-based nitrogen isotope signatures and trophic position (3.50 ± 0.35, mean ± SD). Carbon isotope values indicated that detritus-macroalgae were the dominant carbon source to the food web, with additional contributions from terrestrially derived organic matter and phytoplankton in oligohaline and polyhaline waters, respectively. The main prey of blue crabs ≤49 mm CW were amphipods, shrimp, and unidentified crustaceans, and larger conspecifics fed on bivalves, crabs, and fish. Winter flounder remains, e.g. sagittal otoliths, were identified in the diet of 2.5% of field-collectedmore »blue crabs, whereas PCR-based assays detected winter flounder DNA in 17.7% of crab stomachs. Blue crabs 23 to 160 mm CW preyed on winter flounder ranging from 26 to 66 mm total length, with occurrences of predation most closely associated with increases in crab size. Blue crab predation on winter flounder also varied spatially in the rivers, reflecting site-specific differences in flounder densities, abundances of other preferred prey, and dissolved oxygen concentrations that altered predator-prey dynamics. Lastly, the current predatory impact of blue crabs on juvenile winter flounder is nearly equivalent to other portunid crab species. Anticipated temperature-mediated increases in blue crab densities at northern latitudes, however, will intensify the predator-induced mortality of winter flounder and likely hinder their recovery in southern New England.« less
3. Rapid Genetic Identification of the Blue Crab Callinectes sapidus and Other Callinectes spp. Using Restriction Enzyme Digestion and High Resolution Melt (HRM) Assays

   https://doi.org/10.3389/fmars.2020.00633  

   Lee, B.B ; Schott, E.J. ; Behringer, D.C. ; Bojko, J. ; Kough, A ; Plough, L.V. ( August 2020 , Frontiers in marine science)

   The blue crab Callinectes sapidus is one of the most widely studied marine crustaceans due to its high economic value and ecological significance. Despite extensive research on the blue crab in North America, many questions remain about the distribution and abundance of the species in the subtropics and tropics. In many places, C. sapidus is sympatric with morphologically similar Callinectes spp., which has implications for seafood mislabeling. To enable rapid identification of the species, we designed and tested two PCR-based assays targeting the 12S rRNA mitochondrial gene. The first assay discriminates C. sapidus from other Callinectes spp. via post-PCR restriction digestion (PCR-RFLP) and the second assay discriminates among multiple Callinectes spp. through High Resolution Melting (HRM) analysis and supervised machine learning analyses. A total of 58 DNA samples from five Callinectes spp. (validated via 12S gene sequencing) were used for assay testing. The PCR RFLP assay was 100% accurate identifying C. sapidus from other Callinectes spp. HRM analysis of amplicons showed good discrimination among species, with distinct clusters formed between species with higher sequence homology. Linear discriminant analysis (LDA) classification of HRM curves was quite successful given the small dataset available, producing ∼90–91% mean accuracy in classification over all speciesmore »with 100-fold cross validation. Much of the error came from misclassifications between C. similis and C. danae, which are ∼99% similar in sequence for the amplicon; collapsing them into a single class increased overall classification success to 94%. Error also arose from C. bocourti classifications, which had a reference set containing only three samples. Classification accuracy of C. sapidus alone via HRM was 97.5%. Overall, these assays show great promise as rapid and inexpensive methods to identify Callinectes spp. and have application for both ecological research and seafood identification or labeling.« less
4. Chromosome-level genome assembly of the blue crab, Callinectes sapidus

   https://doi.org/doi.org/10.1093/g3journal/jkab212  

   Bachvaroff, T.R. ( June 2021 , Genes genomes genomics)

   The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200× coverage Illumina paired-end reads, a 60× 8 kb mate-paired library, and 50× PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chromosome scaffolding. The 50 largest scaffolds span 810 Mb are 1.5–37 Mb long and have a repeat content of 36%. The 190 Mb unplaced sequence is in 3921 sequences over 10 kb with a repeat content of 68%. The final assembly N50 is 18.9 Mb for scaffolds and 9317 bases for contigs. Of arthropod BUSCO, ∼88% (888/1013) were complete and single copies. Using 309 million RNAseq read pairs from 12 different tissues and developmental stages, 25,249 protein-coding genes were predicted. Between C. sapidus and Portunus trituberculatus genomes, 41 of 50 large scaffolds had high nucleotide identity and protein-coding synteny, but 9 scaffolds in both assemblies were not clear matches. The protein-coding genes included 9423 one-to-one putative orthologs, ofmore »which 7165 were syntenic between the two crab species. Overall, the two crab genome assemblies show strong similarities at the nucleotide, protein, and chromosome level and verify the blue crab genome as an excellent reference for this important seafood species.« less
5. Hidden similarities in the dynamics of a weakly synchronous marine metapopulation

   https://doi.org/10.1073/pnas.1910964117  

   Rogers, Tanya L. ; Munch, Stephan B. ( December 2019 , Proceedings of the National Academy of Sciences)

   Populations of many marine species are only weakly synchronous, despite coupling through larval dispersal and exposure to synchronous environmental drivers. Although this is often attributed to observation noise, factors including local environmental differences, spatially variable dynamics, and chaos might also reduce or eliminate metapopulation synchrony. To differentiate spatially variable dynamics from similar dynamics driven by spatially variable environments, we applied hierarchical delay embedding. A unique output of this approach, the “dynamic correlation,” quantifies similarity in intrinsic dynamics of populations, independently of whether their abundance is correlated through time. We applied these methods to 17 populations of blue crab (Callinectes sapidus) along the US Atlantic coast and found that their intrinsic dynamics were broadly similar despite largely independent fluctuations in abundance. The weight of evidence suggests that the latitudinal gradient in temperature, filtered through a unimodal response curve, is sufficient to decouple crab populations. As unimodal thermal performance is ubiquitous in ectotherms, we suggest that this may be a general explanation for the weak synchrony observed at large distances in many marine species, although additional studies are needed to test this hypothesis.