Cephalopod research remains limited by the inability to culture species under laboratory conditions for multiple generations to provide continuous access to animals at all stages of the life cycle. ...Here, we describe a multi-generational laboratory culture system for two emerging cephalopod models: the hummingbird or Berry’s bobtail squid,
Euprymna berryi
Sasaki, 1929, and Morse’s bobtail squid,
Euprymna morsei
Verrill, 1881, which are primarily found off mainland Japan.
E. berryi
wild adults were spawned and raised to the third filial generation, and
E. morsei
wild adults were spawned and raised to the second filial generation in a closed system at 20°C. We report growth and survivorship data for a cohort of 30 individuals across the first generation raised in captivity.
E. berryi
and
E. morsei
grew exponentially during the first 90 and 60 days post-hatching, respectively. Survivorship at the first spawning event for
E. berryi
and
E. morsei
was 90% and 77%.
E. berryi
and
E. morsei
females spawned after days 112 and 71 days post-hatching, respectively. We describe the life history of each species and how to distinguish sexes. We discuss the challenges of cephalopod culture and how culturing these species address those problems.
Abstract
Bobtail and bottletail squid are small cephalopods with striking anti-predatory defensive mechanisms, bioluminescence, and complex morphology; that inhabit nektobenthic and pelagic ...environments around the world’s oceans. Yet, the evolution and diversification of these animals remain unclear. Here, we used shallow genome sequencing of thirty-two bobtail and bottletail squids to estimate their evolutionary relationships and divergence time. Our phylogenetic analyses show that each of Sepiadariidae, Sepiolidae, and the three subfamilies of the Sepiolidae are monophyletic. We found that the ancestor of the Sepiolinae very likely possessed a bilobed light organ with bacteriogenic luminescence. Sepiolinae forms a sister group to Rossinae and Heteroteuthinae, and split into Indo-Pacific and Atlantic-Mediterranean lineages. The origin of these lineages coincides with the end of the Tethys Sea and the separation of these regions during the Eocene and the beginning of the Oligocene. We demonstrated that sepiolids radiated after the Late Cretaceous and that major biogeographic events might have shaped their distribution and speciation.
Abstract
Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii ...possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0% of conserved actinopterygian genes, making the quality and completeness of this genome the highest among all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanocyte development) in A. clarkii compared with other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.
Bobtail squid are emerging models for host-microbe interactions, behavior, and development, yet their species diversity and distribution remain poorly characterized. Here, we combine mitochondrial ...and transcriptome sequences with morphological analysis to describe three species of bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu archipelago, and compare them with related taxa. One Ryukyuan type was previously unknown, and is described here as
sp. nov. Another Ryukyuan type is morphologically indistinguishable from
Sasaki, 1913. Molecular analyses, however, place this taxon within the genus
Steenstrup, 1887, and additional morphological investigation led to formal rediagnosis of
and reassignment of this species as
comb. nov. While no adults from the third Ryukyuan type were found, sequences from hatchlings suggest a close relationship with
Reid, 2011, known from Australia and East Timor. The broadly sampled transcriptomes reported here provide a foundation for future phylogenetic and comparative studies.
Two new pygmy squid from the Ryukyu archipelago, Japan, are described:
Kodama jujutsu
, n. gen., n. sp. and
Idiosepius kijimuna
, n. sp. They differ from all other nominal species in a combination of ...traits, including the number of tentacular club suckers, shape of the funnel-mantle locking-cartilage, modification of the male hectocotylus and the structure of the gladius and nuchal-locking cartilage, in addition to mitochondrial DNA markers (12S, 16S and COI). They are both known from Okinawa Island and there is some overlap in their distributions. In a molecular phylogeny that includes all nominal Idiosepiidae,
Kodama jujutsu
, n. gen., n. sp. is sister taxon to a clade containing
Xipholeptos
Reid & Strugnell, 2018 and
Idiosepius
Steenstrup, 1881
. Xipholeptos
and
Idiosepius
are sister taxa.
Idiosepius
spp. now includes seven nominal species. In addition, aspects of the behaviour of the new species are described.
Anthropogenically driven climate change is predicted to increase average sea surface temperatures, as well as the frequency and intensity of marine heatwaves in the future. This increasing ...temperature is predicted to have a range of negative physiological impacts on multiple life-stages of coral reef fish. Nevertheless, studies of early-life stages remain limited, and tissue-specific transcriptomic studies of post-larval coral reef fish are yet to be conducted. Here, in an aquaria-based study we investigate the tissue-specific (brain, liver, muscle, and digestive tract) transcriptomic response of post-larval (20 dph) Amphiprion ocellaris to temperatures associated with future climate change (+3 °C). Additionally, we utilized metatranscriptomic sequencing to investigate how the microbiome of the digestive tract changes at +3 °C. Our results show that the transcriptional response to elevated temperatures is highly tissue-specific, as the number of differentially expressed genes (DEGs) and gene functions varied amongst the brain (102), liver (1785), digestive tract (380), and muscle (447). All tissues displayed DEGs associated with thermal stress, as 23 heat-shock protein genes were upregulated in all tissues. Our results indicate that post-larval clownfish may experience liver fibrosis-like symptoms at +3 °C as genes associated with extracellular matrix structure, oxidative stress, inflammation, glucose transport, and metabolism were all upregulated. We also observe a shift in the digestive tract microbiome community structure, as Vibrio sp. replace Escherichia coli as the dominant bacteria. This shift is coupled with the dysregulation of various genes involved in immune response in the digestive tract. Overall, this study highlights post-larval clownfish will display tissue-specific transcriptomic responses to future increases in temperature, with many potentially harmful pathways activated at +3 °C.
Increasing ocean temperatures have been demonstrated to have a range of negative impacts on coral reef fishes. However, despite a wealth of studies of juvenile/adult reef fish, studies of how early ...developmental stages respond to ocean warming are limited. As overall population persistence is influenced by the development of early life stages, detailed studies of larval responses to ocean warming are essential. Here, in an aquaria-based study we investigate how temperatures associated with future warming and present-day marine heatwaves (+3 °C) impact the growth, metabolic rate, and transcriptome of 6 discrete developmental stages of clownfish larvae (Amphiprion ocellaris). A total of 6 clutches of larvae were assessed, with 897 larvae imaged, 262 larvae undergoing metabolic testing and 108 larvae subject to transcriptome sequencing. Our results show that larvae reared at +3 °C grow and develop significantly faster and exhibit higher metabolic rates than those in control conditions. Finally, we highlight the molecular mechanisms underpinning the response of larvae from different developmental stages to higher temperatures, with genes associated with metabolism, neurotransmission, heat stress and epigenetic reprogramming differentially expressed at +3 °C. Overall, these results indicate that clownfish development could be altered under future warming, with developmental rate, metabolic rate, and gene expression all affected. Such changes may lead to altered larval dispersal, changes in settlement time and increased energetic costs.
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•Clownfish larvae were reared at temperatures associated with future ocean warming.•Larvae display faster growth and development, and higher metabolic rates at +3 °C.•Larvae have >450 differentially expressed genes throughout development at +3 °C.•Altered expression of genes involved in heat-stress and epigenetic modifications•Clownfish development will be altered at physiological and molecular level at +3 °C.
Many female squids and cuttlefishes have a symbiotic reproductive organ called the accessory nidamental gland (ANG) that hosts a bacterial consortium involved with egg defense against pathogens and ...fouling organisms. While the ANG is found in multiple cephalopod families, little is known about the global microbial diversity of these ANG bacterial symbionts. We used 16S rRNA gene community analysis to characterize the ANG microbiome from different cephalopod species and assess the relationship between host and symbiont phylogenies. The ANG microbiome of 11 species of cephalopods from four families (superorder: Decapodiformes) that span seven geographic locations was characterized. Bacteria of class
, and
were found in all species, yet analysis of amplicon sequence variants by multiple distance metrics revealed a significant difference between ANG microbiomes of cephalopod families (weighted/unweighted UniFrac, Bray-Curtis,
= 0.001). Despite being collected from widely disparate geographic locations, members of the family Sepiolidae (bobtail squid) shared many bacterial taxa including (~50%)
(Verrucomicrobia) and
(Alphaproteobacteria) species. Furthermore, we tested for phylosymbiosis and found a positive correlation between host phylogenetic distance and bacterial community dissimilarity (Mantel test
= 0.7). These data suggest that closely related sepiolids select for distinct symbionts from similar bacterial taxa. Overall, the ANGs of different cephalopod species harbor distinct microbiomes and thus offer a diverse symbiont community to explore antimicrobial activity and other functional roles in host fitness.IMPORTANCEMany aquatic organisms recruit microbial symbionts from the environment that provide a variety of functions, including defense from pathogens. Some female cephalopods (squids, bobtail squids, and cuttlefish) have a reproductive organ called the accessory nidamental gland (ANG) that contains a bacterial consortium that protects eggs from pathogens. Despite the wide distribution of these cephalopods, whether they share similar microbiomes is unknown. Here, we studied the microbial diversity of the ANG in 11 species of cephalopods distributed over a broad geographic range and representing 15-120 million years of host divergence. The ANG microbiomes shared some bacterial taxa, but each cephalopod species had unique symbiotic members. Additionally, analysis of host-symbiont phylogenies suggests that the evolutionary histories of the partners have been important in shaping the ANG microbiome. This study advances our knowledge of cephalopod-bacteria relationships and provides a foundation to explore defensive symbionts in other systems.
Bobtail squid are emerging models for host-microbe interactions, behavior, and development, yet their species diversity and distribution remain poorly characterized. Here, we combine mitochondrial ...and transcriptome sequences with morphological analysis to describe three species of bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu archipelago, and compare them with related taxa. One Ryukyuan type was previously unknown, and is described here as Euprymna brenneri sp. nov. Another Ryukyuan type is morphologically indistinguishable from Sepiola parva Sasaki, 1913. Molecular analyses, however, place this taxon within the genus Euprymna Steenstrup, 1887, and additional morphological investigation led to formal rediagnosis of Euprymna and reassignment of this species as Euprymna parva comb. nov. While no adults from the third Ryukyuan type were found, sequences from hatchlings suggest a close relationship with E. pardalota Reid, 2011, known from Australia and East Timor. The broadly sampled transcriptomes reported here provide a foundation for future phylogenetic and comparative studies.
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