Trimethylamine N-Oxide (TMAO) and Trimethylamine (TMA) Determinations of Two Hadal Amphipods

The amphipod genome reveals population dynamics and adaptations to hadal environment

The amphipod Hirondellea gigas is a dominant species inhabiting the deepest part of the ocean (∼6,800-11,000 m), but little is known about its genetic adaptation and population dynamics. Here, we present a chromosome-level genome of H. gigas, characterized by a large genome size of 13.92 Gb. Whole-genome sequencing of 510 individuals from the Mariana Trench indicates no population differentiation across depths, suggesting its capacity to tolerate hydrostatic pressure across wide ranges. H. gigas in the West Philippine Basin is genetically divergent from the Mariana and Yap Trenches, suggesting genetic isolation attributed to the geographic separation of hadal features. A drastic reduction in effective population size potentially reflects glacial-interglacial changes. By integrating multi-omics analysis, we propose host-symbiotic microbial interactions may be crucial in the adaptation of H. gigas to the extremely high-pressure and food-limited environment. Our findings provide clues for adaptation to the hadal zone and population genetics.

Reaction-Based Fluorescence Assays for the Determination of Food Trimethylamine Oxide

Trimethylamine oxide (TMAO), a microbial metabolite commonly found in foods, has been attracting increasing attention as it is associated with the risk of several diseases. Simple and accurate analytical methods are crucial for TMAO study. In the present study, we proposed a chemical reaction-based fluorescence assay for TMAO detection using synthetic small molecular probes. After systematic screening and optimization, the sensitive and selective quantification of TMAO has been achieved based on a fluorescence probe P6 (3-iodopropanyl group modified resorufin). Excellent linearity (R2 = 0.997) was found between 6.25 and 50 μM, and the limit of detection (LOD) was 0.20 μM. Using this method, TMAO levels in several marine fishes and shellfishes have been successfully analyzed. The probe-based assay offers a simple and useful way for TMAO determination. The design is inspired by the unique oxidation reaction between TMAO and halogen, which opens a new perspective in the development of more advanced analytical assays for TMAO in the future.

Genome sequencing of Coryphaenoides yaquinae reveals convergent and lineage-specific molecular evolution in deep-sea adaptation

Abyssal (3501-6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome-level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal-living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep-sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep-sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin-containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep-sea species shed new light on the common genetic innovations required for deep-sea adaptation by the fishes.

Morphological and molecular evolution of hadal amphipod’s eggs provides insights into embryogenesis under high hydrostatic pressure

Hadal zones are unique habitats characterized by high hydrostatic pressure (HHP) and scarce food supplies. The ability of eggs of species dwelling in hadal zones to develop into normal embryo under high hydrostatic pressure is an important evolutionary and developmental trait. However, the mechanisms underlying the development of eggs of hadal-dwelling species remain unknown due to the difficulty of sampling ovigerous females. Here, morphological and transcriptome analyses of eggs of the “supergiant” amphipod Alicella gigantea collected from the New Britain Trench were conducted. The morphology of A. gigantea eggs, including size, was assessed and the ultrastructure of the eggshell was investigated by scanning electron microscopy. Transcriptome sequencing and molecular adaptive evolution analysis of A. gigantea eggs showed that, as compared with shallow-water Gammarus species, genes exhibiting accelerated evolution and the positively selected genes were mostly related to pathways associated with “mitosis” and “chitin-based embryonic cuticle biosynthetic process”, suggesting that “normal mitosis maintenance” and “cuticle development and protection” are the two main adaptation strategies for survival of eggs in hadal environments. In addition, the concentration of trimethylamine oxide (TMAO), an important osmotic regulator, was significantly higher in the eggs of hadal amphipods as compared to those of shallow-water species, which might promote the eggs’ adaptation abilities. Morphological identification, evolutionary analysis, and the trimethylamine oxide concentration of A. gigantea eggs will facilitate a comprehensive overview of the piezophilic adaptation of embryos in hadal environments and provide a strategy to analyze embryogenesis under high hydrostatic pressure.

Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors

The seas confront organisms with a suite of abiotic stressors that pose challenges for physiological activity. Variations in temperature, hydrostatic pressure, and salinity have potential to disrupt structures, and functions of all molecular systems on which life depends. During evolution, sequences of nucleic acids and proteins are adaptively modified to "fit" these macromolecules for function under the particular abiotic conditions of the habitat. Complementing these macromolecular adaptations are alterations in compositions of solutions that bathe macromolecules and affect stabilities of their higher order structures. A primary result of these "micromolecular" adaptations is preservation of optimal balances between conformational rigidity and flexibility of macromolecules. Micromolecular adaptations involve several families of organic osmolytes, with varying effects on macromolecular stability. A given type of osmolyte generally has similar effects on DNA, RNA, proteins and membranes; thus, adaptive regulation of cellular osmolyte pools has a global effect on macromolecules. These effects are mediated largely through influences of osmolytes and macromolecules on water structure and activity. Acclimatory micromolecular responses are often critical in enabling organisms to cope with environmental changes during their lifetimes, for example, during vertical migration in the water column. A species' breadth of environmental tolerance may depend on how effectively it can vary the osmolyte composition of its cellular fluids in the face of stress. Micromolecular adaptations remain an under-appreciated aspect of evolution and acclimatization. Further study can lead to a better understanding of determinants of environmental tolerance ranges and to biotechnological advances in designing improved stabilizers for biological materials.