Amynthas corticis genome reveals molecular mechanisms behind global distribution

Acceleration of genome rearrangement in clitellate annelids

Comparisons of multiple metazoan genomes have revealed the existence of ancestral linkage groups (ALGs), genomic scaffolds sharing sets of orthologous genes that have been inherited from ancestral animals for hundreds of millions of years (Simakov et al. 2022; Schultz et al. 2023) These ALGs have persisted across major animal taxa including Cnidaria, Deuterostomia, Ecdysozoa and Spiralia. Notwithstanding this general trend of chromosome-scale conservation, ALGs have been obliterated by extensive genome rearrangements in certain groups, most notably including Clitellata (oligochaetes and leeches), a group of easily overlooked invertebrates that is of tremendous ecological, agricultural and economic importance (Charles 2019; Barrett 2016). To further investigate these rearrangements, we have undertaken a comparison of 12 clitellate genomes (including four newly sequenced species) and 11 outgroup representatives. We show that these rearrangements began at the base of the Clitellata (rather than progressing gradually throughout polychaete annelids), that the inter-chromosomal rearrangements continue in several clitellate lineages and that these events have substantially shaped the evolution of the otherwise highly conserved Hox cluster.

Gut toxicity of polystyrene microplastics and polychlorinated biphenyls to Eisenia fetida: Single and co-exposure effects with a focus on links between gut bacteria and bacterial translocation stemming from gut barrier damage

Microplastics' (MPs) ability to sorb and transport polychlorinated biphenyls (PCBs) in soil ecosystems warrants significant attention. Although organisms mainly encounter pollutants through the gut, the combined pollution impact of MPs and PCBs on soil fauna gut toxicity remains incompletely understood. Consequently, this study examined the gut toxicity of polystyrene MPs (PS-MPs) and PCB126 on Eisenia fetida, emphasizing the links between gut bacteria and bacterial translocation instigated by gut barrier impairment. Our findings underscored that E. fetida could ingest PS-MPs, which mitigated the PCB126 accumulation in E. fetida by 9.43 %. Exposure to PCB126 inhibited the expression of gut tight junction (TJ) protein genes. Although the presence of PS-MPs attenuated this suppression, it didn't alleviate gut barrier damage and bacterial translocation in the co-exposure group. This group demonstrated a significantly increased level of gut bacterial load (BLT, ANOVA, p = 0.005 vs control group) and lipopolysaccharide-binding protein (LBP, ANOVA, all p < 0.001 vs control, PCB, and PS groups), both of which displayed significant positive correlations with antibacterial defense. Furthermore, exposure to PS-MPs and PCB126, particularly within the co-exposure group, results in a marked decline in the dispersal ability of gut bacteria. This leads to dysbiosis (Adonis, R2 = 0.294, p = 0.001), with remarkable signature taxa such as Janthinobacterium, Microbacterium and Pseudomonas, being implicated in gut barrier dysfunction. This research illuminates the mechanism of gut toxicity induced by PS-MPs and PCB126 combined pollution in earthworms, providing novel insights for the ecological risk assessment of soil.

Division of developmental phases of freshwater leech Whitmania pigra and key genes related to neurogenesis revealed by whole genome and transcriptome analysis

The freshwater leech Whitmania pigra (W. pigra) Whitman (Annelida phylum) is a model organism for neurodevelopmental studies. However, molecular biology research on its embryonic development is still scarce. Here, we described a series of developmental stages of the W. pigra embryos and defined five broad stages of embryogenesis: cleavage stages, blastocyst stage, gastrula stage, organogenesis and refinement, juvenile. We obtained a total of 239.64 Gb transcriptome data of eight representative developmental phases of embryos (from blastocyst stage to maturity), which was then assembled into 21,482 unigenes according to our reference genome sequenced by single-molecule real-time (SMRT) long-read sequencing. We found 3114 genes differentially expressed during the eight phases with phase-specific expression pattern. Using a comprehensive transcriptome dataset, we demonstrated that 57, 49 and 77 DEGs were respectively related to morphogenesis, signal pathways and neurogenesis. 49 DEGs related to signal pathways included 30 wnt genes, 14 notch genes, and 5 hedgehog genes. In particular, we found a cluster consisting of 7 genes related to signal pathways as well as synapses, which were essential for regulating embryonic development. Eight genes cooperatively participated in regulating neurogenesis. Our results reveal the whole picture of W. pigra development mechanism from the perspective of transcriptome and provide new clues for organogenesis and neurodevelopmental studies of Annelida species.

Molecular insights into high-altitude adaption and acclimatisation of Aporrectodea caliginosa

A megabase genome assembly for Aporrectodea caliginosa is presented with transcriptomic and SNP-based evidence for acclimatisation and adaption to extreme weather conditions found at high altitude.

Here, we explore the high-altitude adaptions and acclimatisation of Aporrectodea caliginosa. Population diversity is assessed through mitochondrial barcoding, identifying closely related populations across the island of Pico (Azores). We present the first megabase N50 assembly size (1.2 Mbp) genome for A. caliginosa. High- and low-altitude populations were exposed experimentally to a range of oxygen and temperature conditions, simulating altitudinal conditions, and the transcriptomic responses explored. SNP densities are assessed to identify signatures of selective pressure and their link to differentially expressed genes. The high-altitude A. caliginosa population had lower differential expression and fewer co-expressed genes between conditions, indicating a more condition-refined epigenetic response. Genes identified as under adaptive pressure through F_st and nucleotide diversity in the high-altitude population clustered around the differentially expressed an upstream environmental response control gene, HMGB1. The high-altitude population of A. caliginosa indicated adaption and acclimatisation to high-altitude conditions and suggested resilience to extreme weather events. This mechanistic understanding could help offer a strategy in further identifying other species capable of maintaining soil fertility in extreme environments.

Biochemical, transcriptomic, gut microbiome responses and defense mechanisms of the earthworm Eisenia fetida to salt stress

The accumulation of sodium chloride (NaCl) in soil is a worldwide problem with detrimental effects on the survival of soil animals. The effects of NaCl on earthworms remain unclear. Here, we show that the growth rate, cocoon production rate, annetocin precursor (ANN) mRNA level, and superoxide dismutase and catalase activities in earthworms were reduced under NaCl stress, whereas the mortality rate, reactive oxygen species (ROS) and malondialdehyde activity level increased. Histological damage to the earthworm body wall and intestine were observed under NaCl stress. NaCl stress increased DNA damage in the seminal vesicle and coelomocytes. The mRNA level of lumbrokinase, 1,3-beta-glucanse, coelomic cytolytic factor (CCF1), and alpha-amylase was significantly down-regulated, whereas that of earthworm excitatory peptides2 (EEP2) was up-regulated. From 16 S rRNA sequencing, the earthworm gut microbiota diversity decreased under NaCl stress. However, Verminephrobacter, Kluyvera, Lactobacillus, and Ochrobactrum increased under NaCl stress. These findings contribute to the risk assessment of the salt stress on soil organisms.

Polystyrene microplastics impact the occurrence of antibiotic resistance genes in earthworms by size-dependent toxic effects

Microplastics (MPs) and antibiotic resistance genes (ARGs) are two classes of emerging and prevalent contaminants in terrestrial environments. To date, effects of MPs on the occurrence of ARGs in terrestrial invertebrates remain uncertain. Here we exposed earthworms to a soil amended with polystyrene MPs at two environmentally relevant concentrations to elucidate the occurrence and mechanisms of ARGs in earthworms impacted by MPs with different sizes. Nano-size and 10 mg/kg of 100 µm MPs slightly affected the occurrence of ARGs in earthworms. Highest abundance of ARGs was found in the presence of 10 mg/kg of 10 µm MPs, whereas 100 mg/kg of 10 µm MPs significantly changed the profile of ARGs. Metagenomics sequencing and toxicity tests indicated that MPs caused toxicity and influenced the abundance of microbial community in earthworms, resulting in the changes of ARGs. Results of proteomics and metabolomics demonstrated that 100 mg/kg of 10 µm MPs changed the microenvironment of earthworm gut, built a new homeostatic process, and thus increased the abundance of key bacterial that carried a variety of ARGs. This study highlights the size-dependent toxic effects of MPs and their impacts on the transfer of ARGs in terrestrial environments.