Li-Sheng He

Background: Hyaluronan synthases (HASs) are ubiquitous in living organisms, and the hyaluronic acid (HA) synthesized by them are important to their body and well used in medicine, cosmetics and other fields. HAS from deep-sea creatures has not yet been explored before. The study aims to analyse the characteristics and enzyme kinetics of a novel hyaluronan synthase derived from the symbiont “Candidatus Mycoplasma liparidae” found in deep-sea snailfish (snHAS). Methodology: snHAS was over-expressed using His ₆ as tag in the study. The sequence alignment was conducted by Cluster W and then the phylogenetic analyse of HASs was performed by Mega 6.0 to investigate the position of snHAS during evolution. K_m and V_max were detected to study the enzyme kinetics of snHAS wildtype and its mutant. The molecular weight of HA was evaluated by high performance gel permeation chromatography (HPGPC). The cardiolipin was added to investigate whether it had a promoting effect on the snHAS. Results: The length of snHAS was 933 bp with an open reading frame (ORF) of 310 amino acids. Unlike other repoted HASs, snHAS had no transmembrane region and was not classified into the currently known Class I or Class II. snHAS could synthesize hyaluronan with lower molecular weights using the substrates of uridine-diphosphate—N-acetylglucosamine (UDP-GlcNAc) and uridine-diphosphate—glucuronic acid (UDP-GlcA) in vitro. The K_m values of snHAS were 258 ± 45 µM and 39 ± 5 µM for UDP-GlcNAc and UDP-GlcA, respectively, much lower than those from mice (K_m for UDP-GlcA: 55 ± 5 µM; K_m for UDP-GlcNAc: 870 ± 60 µM). The k_cat/K_m values of snHAS were 163.5 s⁻¹ mM⁻¹ and 8.08 s⁻¹ mM⁻¹ for UDP-GlcA and UDP-GlcNAc, respectively. Furthermore, the activity of snHAS was independent of cardiolipin. Conclusions: snHAS was a novel HAS based on the characteristics of the animo acid sequence, which could produce low molecular weight of HA with high efficiency. This provides a molecular basis for the biosynthesis of low molecular weight of HA.

Small proteins (SPs, ≤50 amino acids) are usually ignored by automated bioinformatic algorithms and difficult to be detected by traditional protein purification. In this study, 193,281 prokaryotic SP clusters were generated using 433,311 small open reading frames (sORFs) predicted in assemblies of 71 full-ocean-depth marine water metagenomes from the western pacific. Further filtration with at least 5 copies per million reads resulted in 75,581 prevalent SP clusters, among which 4,307 clusters have coding capacity as predicted by RNAcode. For these RNAcode-filtered SP (RfSP) clusters hosted largely by Proteobacteria, Thaumarchaeota and Marinimicrobia, 29.16% of them show homology () in all prokaryotic genomes. About 2% of the RfSP clusters were estimated as potential antimicrobial peptides and were distributed across all depth zones. Transcription of 7.96% of the RfSP clusters was verified in 12 deep-sea metatranscriptomes, and translation of 34 prevalent SP clusters was detected in 14 metaproteomes. The transcribed RfSP clusters are involved in processes such as DNA stability under stress condition, betaine transport and cell division regulation for a rapid response to varying deep-sea environments. This study uncovers a vast reservoir of SPs with pivotal functions in potential antibiotic activities, hyperoxide detoxification and pressure resistance for fitness of marine prokaryotes in deep ocean.

Small proteins (SPs, ≤ 50 amino acids) are usually ignored by automated bioinformatic algorithms and difficult to be detected by traditional protein purification. In this study, 193,281 prokaryotic SP clusters were generated using 433,311 small open reading frames (sORFs) predicted in assemblies of 71 full-ocean-depth marine water metagenomes from the western pacific. Further filtration with at least 5 copies per million reads resulted in 75,581 prevalent SP clusters, among which 4,307 clusters have coding capacity as predicted by RNAcode. For these RNAcode-filtered SP (RfSP) clusters hosted largely by Proteobacteria, Thaumarchaeota and Marinimicrobia, 29.16% of them show homology () in all prokaryotic genomes. About 2% of the RfSP clusters were estimated as potential antimicrobial peptides and were distributed across all depth zones. Transcription of 7.96% of the RfSP clusters was verified in 12 deep-sea metatranscriptomes, and translation of 34 prevalent SP clusters was detected in 14 metaproteomes. The transcribed RfSP clusters are involved in processes such as DNA stability under stress condition, betaine transport and cell division regulation for a rapid response to varying deep-sea environments. This study uncovers a vast reservoir of SPs with pivotal functions in potential antibiotic activities, hyperoxide detoxification and pressure resistance for fitness of marine prokaryotes in deep ocean.

Hagfishes are fascinating creatures that typically inhabit the deep sea. The deep sea is characterized by its lack of sunlight, primary productivity, and diminishing biomass with increasing ocean depth. Therefore, hagfishes living in this environment must develop effective survival strategies to adapt to the limited food supply. Deep-sea hagfishes have been observed to survive without food intake for up to one year. In this study, we have assembled a high-quality somatic genome of the deep-sea hagfish (Eptatretus okinoseanus) captured below 1,000 m. We compared the genome of E. okinoseanus with the genomes of inshore hagfish, lampreys, and other related species to investigate the genetic factors underlying the deep-sea hagfish adaptations to the environment. The E. okinoseanus somatic genome was estimated to be 1.89 Gb and assembled into 17 pseudochromosomes. Phylogenetic analysis showed that shallow-sea and deep-sea hagfishes diverged approximately 58.8 million years ago. We found Perilipin gene family was significantly expanded in deep sea E. okinoseanus, which promotes triacylglycerol storage. Furthermore, a series of genes involved in fatty acid synthesis and metabolism, blood glucose regulation, and metabolic rate regulation were also expanded, rapid evolution or positive selection, and these changes contribute to their efficiency in energy utilization. Among these genes, the positively selected gene JNK may play an important role in energy metabolism. In addition, the olfactory receptors of the deep-sea hagfish were significantly expanded to 86, and three conserved motifs present only in hagfishes olfactory receptors were identified, which may facilitate the rapid localization of carrion. This study provides valuable genomic resources for insights into the survival strategies of deep-sea hagfishes in oligotrophic environments.

It is relatively poorly understood how vertebrates can survive and thrive in deep-sea environments (depths below 3,400 m that are characterized by high hydrostatic pressures, low temperatures, and sparse food resources). Here we report two high-quality chromosome-level genomes for deep-sea eels (Ilyophis sp1 and Ilyophis sp2). Combining Illumina reads, PacBio, and Hi-C technologies, we sequenced and assembled its genomes. The genome assemblies were 1494.88 Mb and 1469.15 Mb for Ilyophis sp1 and Ilyophis sp2, with scaffold N50 values of 121.13 Mb and 115.31 Mb, and genome annotation predicted 22,465 and 21,632 protein-coding genes respectively. Phylogenetic analyses indicated that these two deep-sea eels diverged from European eels ~111.9 million years ago (Mya) and likely evolved into two separate groups ~3.59 Mya. Comparative genomic analyses reveal that: (1) the positively selected cytoskeleton gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability under high pressure; (2) the changes in protein sequences of Acox1 may enhance cell membrane fluidity and maintain transport activity under high pressure; (3) functional mutation of the translation gene HARS in deep-sea eels may change its translation ability to resist the influence of low temperature on translation-related enzymes; and (4) energy metabolism under a food-limited environment may be increased by expanded and positively selected gene enrichment in AMPK and mTOR signaling pathways. This study provides insights into the underlying genetic basis and molecular evolution of deep-sea vertebrates and provides valuable genomic resources for future investigations of deep-sea biology. Keywords: deep-sea, eels, Ilyophis, adaption, high hydrostatic pressure.

Deep-sea eukaryotic microorganisms play a vital role in degrading organic matter and geochemically cycling elements in the deep ocean. However, the impact of sampling methods on detection of these microorganisms under high hydrostatic pressure remains uncertain. In this study, we compared a traditional water sampling method using a Niskin bottle, an in situ microbial filtration and fixation method (ISMIFF), and a multiple in situ nucleic acid collection (MISNAC) method to exhibit differences in the community structures that were collected at ~590–3100 m in the South China Sea (SCS). The classification and biodiversity indices of 18S rDNA Illumina sequencing reads from the V9 variation region revealed higher diversity for MISNAC DNA absorption column samples compared to others. Importantly, the relative abundance of Ciliophora (19.49%), Copepoda (23.31%), and Diplonemea (10.67%) was higher in MISNAC adsorption column samples, while Retaria (48.86%) were dominant in the MISNAC membrane samples. This indicates that MISNAC columns might collect more DNA in situ for the naked protists, while Retaria with a carbonate shell were more likely retained on the membrane. In conclusion, MISNAC is an effective method for DNA collection of deep-sea eukaryotic microorganisms and provides valuable materials for studying deep-sea microbial ecosystems.

As the deepest vertebrate in the ocean, the hadal snailfish (Pseudoliparis swirei), which lives at a depth of 6,000–8,000 m, is a representative case for studying adaptation to extreme environments. Despite some preliminary studies on this species in recent years, including their loss of pigmentation, visual and skeletal calcification genes, and the role of trimethylamine N-oxide in adaptation to high-hydrostatic pressure, it is still unknown how they evolved and why they are among the few vertebrate species that have successfully adapted to the deep-sea environment. Using genomic data from different trenches, we found that the hadal snailfish may have entered and fully adapted to such extreme environments only in the last few million years. Meanwhile, phylogenetic relationships show that they spread into different trenches in the Pacific Ocean within a million years. Comparative genomic analysis has also revealed that the genes associated with perception, circadian rhythms, and metabolism have been extensively modified in the hadal snailfish to adapt to its unique environment. More importantly, the tandem duplication of a gene encoding ferritin significantly increased their tolerance to reactive oxygen species, which may be one of the important factors in their adaptation to high-hydrostatic pressure.

Amphipods are an important group of invertebrates in marine ecosystems due to their high abundance and diversity. As an essential part of the marine food web, amphipods play a vital role in nutrient recycling and provide large amounts of detritus-derived fine-particulate organic matter for other invertebrates. Although the importance of gut microbiota and the necessity to consider them has been increasingly recognized, the gut microbial community and diversity of amphipods have not been well studied. Here, we comparatively studied the gut microbiota of diverse amphipod species inhabiting from coastal to hadopelagic zones. The results showed that four phyla, including Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota, occupied more than 90% of the total microbes in the studied amphipod guts, with Firmicutes being dominant in the hadal amphipods. The gut microbiome of amphipods from the hadal zone displayed the lowest richness, lowest diversity, and shared few microorganisms with the surrounding seawater compared to others. Amphipods in different inhabiting regions have discriminant taxa for their gut microbial communities. Taken together, amphipod gut microbiota was affected by both biological and abiotic factors, yet these factors are not independent. This article provides us with a further understanding of the structure and characteristics of the gut microbiota of invertebrate organisms.

The genus Rimicaris is the dominant organism living in hydrothermal vents. However, little research has been done on the functions of their intestinal flora. Here, we investigated the potential functions of Deferribacterota, which is dominant in the intestine of Rimicaris kairei from the Central Indian Ridge. In total, six metagenome-assembled genomes (MAGs) of Deferribacterota were obtained using the metagenomic approach. The six Deferribacterota MAGs (Def-MAGs) were clustered into a new branch in the phylogenetic tree. The six Def-MAGs were further classified into three species, including one new order and two new genera, based on the results of phylogenetic analysis, relative evolutionary divergence (RED), average nucleotide identity (ANI), average amino acid identity (AAI) and DNA–DNA hybridization (DDH) values. The results of the energy metabolism study showed that these bacteria can use a variety of carbon sources, such as glycogen, sucrose, salicin, arbutin, glucose, cellobiose, and maltose. These bacteria have a type II secretion system and effector proteins that can transport some intracellular toxins to the extracellular compartment and a type V CRISPR–Cas system that can defend against various invasions. In addition, cofactors such as biotin, riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) synthesized by R. kairei gut Deferribacterota may also assist their host in surviving under extreme conditions. Taken together, the potential function of Deferribacterota in the hydrothermal R. kairei gut suggests its long-term coevolution with the host.