Echinoderms exhibit several fascinating evolutionary innovations that are rarely seen in the animal kingdom, but how these animals attained such features is not well understood. Here we report the sequencing and analysis of the genome and extensive transcriptomes of the sea cucumber Apostichopus japonicus, a species from a special echinoderm group with extraordinary potential for saponin synthesis, aestivation and organ regeneration. The sea cucumber does not possess a reorganized Hox cluster as previously assumed for all echinoderms, and the spatial expression of Hox7 and Hox11/13b potentially guides the embryo-to-larva axial transformation. Contrary to the typical production of lanosterol in animal cholesterol synthesis, the oxidosqualene cyclase of sea cucumber produces parkeol for saponin synthesis and has “plant-like” motifs suggestive of convergent evolution. The transcriptional factors Klf2 and Egr1 are identified as key regulators of aestivation, probably exerting their effects through a clock gene-controlled process. Intestinal hypometabolism during aestivation is driven by the DNA hypermethylation of various metabolic gene pathways, whereas the transcriptional network of intestine regeneration involves diverse signaling pathways, including Wnt, Hippo and FGF. Decoding the sea cucumber genome provides a new avenue for an in-depth understanding of the extraordinary features of sea cucumbers and other echinoderms.

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Antibiotic resistance genes (ARGs) are globally prevalent in mariculture sediment, and their presence is an issue of concern in the context of antibiotic use. Although large amounts of fishmeal have been released into the sediment, the role of fishmeal in ARG dissemination remains unclear. In this study, high-throughput ARG profiles in representative fishmeal products and the impact of fishmeal on the sediment resistome were investigated. A total of 132 unique ARGs and 4 mobile genetic elements (MGEs) were detected in five fishmeal products. ARG abundance and diversity in the mariculture microcosm sediment were significantly increased by the addition of fishmeal, and trends in ARG patterns correlated with the resident bacterial community in sediment (P < 0.05). After DNase treatment of fishmeal removed 84.3% of total ARGs, the remaining nutrients in fishmeal increased the relative abundance but not the diversity of ARGs in microcosm sediment. Our study has revealed for the first time that fishmeal itself is a major reservoir for ARGs, and the shift in the bacterial community induced by the nutrients in fishmeal is the main driver shaping the resistome in mariculture microcosm sediment. Our findings caution against the previously unperceived risk of ARG propagation in fishmeal-receiving ecosystems.

Summary A growing body of evidence suggests that microplastics may be colonized with a unique microbiome, termed ‘plastisphere’, in aquatic environments. However, the deep mechanisms (deterministic and/or stochastic processes) underlying the community assembly on microplastics are still poorly understood. Here, we took the estuary of Hangzhou Bay (Zhejiang, China) as an example and examined the assembly mechanisms of bacterial communities in water and microplastic samples. Results from high‐throughput sequencing showed that Proteobacteria, Firmicutes, and Actinobacteria were the dominant phyla across all samples. Additionally, microorganisms from plastisphere and planktonic communities exhibited contrasting taxonomic compositions, with greater within‐group variation for microplastic samples. The null model analysis indicated the plastisphere bacterial communities were dominantly driven by the stochastic process of drift (58.34%) and dispersal limitation (23.41%). The normalized stochasticity ratio (NST) also showed that the community assembly on microplastics was more stochastic (NST > 50%). Based on the Sloan neutral community model, the migration rate for plastisphere communities (0.015) was significantly lower than that for planktonic communities (0.936), potentially suggesting that it is the stochastic balance between loss and gain of bacteria (e.g., stochastic births and deaths) critically shaping the community assembly on microplastics and generating the specific niches. This study greatly enhanced our understanding of the ecological patterns of microplastic‐associated microbial communities in aquatic environments.

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