Teleost fishes are a highly diverse and ecologically essential group of aquatic vertebrates and include coho salmon, Onchorhynchus kisutch. Coho are semelparous and all ovarian follicles develop synchronously. Owing to their ubiquitous distribution, teleost provide critical sources of food worldwide through subsistence, commercial fisheries, and aquaculture. Enhancement of commercial hatchery practices requires a detailed knowledge of teleost reproductive physiology. Despite decades of research on teleost reproductive processes, an in-depth proteome of teleost ovarian development has yet to be generated. We describe a coho salmon ovarian proteome of over 5700 proteins, generated with data independent acquisition, revealing the suite of detectable proteins that change through the transition from primary to secondary ovarian follicle development. This transition is critical for puberty onset, egg quality, and further embryonic development. Primary ovarian follicle development was marked by differential abundances of proteins involved in carbohydrate metabolism, protein turnover, and the complement pathway, suggesting elevated metabolism as the oocytes enter maturation. The greatest proteomic shift occurred during the transition from primary to secondary follicle growth, with increased abundance of proteins underlying cortical alveoli formation, extracellular matrix reorganization, iron binding, and cell-cell signaling. This work provides a foundation for identifying biomarkers of salmon oocyte stage and quality.

Field studies at terrestrial analogue sites represent an important contribution to the science of ocean worlds. The value of the science and technology investigations conducted at field analogue sites depends on the relevance of the analogue environment to the target ocean world. We accept that there are no perfect analogues for many of the unique environments represented by ocean worlds but suggest that a one-to-one matching of environmental characteristics and conditions is not crucial to the success or impact of the work. Instead, we must instead determine which processes and parameters are required to map directly to the target ocean world environment with high fidelity to address the science question or engineering challenge. Where there are discrepancies between the model and target environment, we must fully understand how those limitations impact the applicability of the study, and mitigate these where possible using alternative approaches. Here we present a two-step approach to 1) identify the most crucial processes and parameters associated with a given science question and 2) assess the fidelity of these processes and parameters at a proposed field site to those expected for the target ocean world. We demonstrate this approach in a test case evaluating three types of ocean world analogue environments with respect to a science question. Our proposed framework will not only enhance the scientific rigor of field research but also provide access to a broader range of field sites relevant to ocean worlds processes, enabling a greater diversity of ocean and geological science researchers.

Zooplankton undergo a vertical migration which exposes them to gradients of light, temperature, oxygen and food availability on a predictable daily schedule. Anticipating and responding to these environmental conditions, which independently are known to influence metabolic rates, likely has an appreciable effect on the delivery of waste products to the distinctly different daytime (deep) and nighttime (surface) habitats. Disentangling the co-varying and potentially synergistic interactions on metabolic rates has proven difficult, despite the importance of this migration to oceanic biogeochemical cycling. This study examines the transcriptomic and proteomic profile of the circumglobal migratory copepod, Pleuromamma xiphias, over the diel cycle. The transcriptome showed a large number of up-regulated genes during the middle of the day – the period often considered to be of lowest metabolic activity. There were proteomic and transcriptomic peaks in oxidative stress response and muscle proteins after the periods of migration, suggestive of a physiological consequence of migration. There were changes in metabolic pathways over time, with increased ammonium production signals during the evening and chitin synthesis and degradation pathways during the day. Comparisons of patterns across the paired datasets suggest that 1) estimates of physiological rates made in the laboratory in steady state conditions that don’t account for time of day may not be adequate to predict in situ phenotypes 2) use of ‘omics datasets to predict organismal phenotypes must be done cautiously as highly dynamic patterns in the transcriptome and proteome are often dampened and sometimes asynchronous at the enzyme or organismal level.

The necessity to understand the influence of global ocean change on biota has exposed wide-ranging gaps in our knowledge of the fundamental principles that underpin marine life. Concurrently, physiological research has stagnated, in part driven by the advent and rapid evolution of molecular biological techniques, such that they now influence all lines of enquiry in biological and microbial oceanography. This dominance has led to an implicit assumption that physiology is outmoded, and advocacy that ecological and biogeochemical models can be directly informed by omics. However, the main modelling currencies continue to be biological rates and biogeochemical fluxes. Here we ask: how do we translate the wealth of information on physiological potential from omics-based studies to quantifiable physiological rates and, ultimately, to biogeochemical fluxes? Based on the trajectory of the state-of-the-art in biomedical sciences, along with case-studies from ocean sciences, we conclude that it is unlikely that omics can provide such rates in the coming decade. Thus, while physiological rates will continue to be central to providing projections of global change biology, we must revisit the metrics we rely upon. We advocate for the co-design of a new generation of rate measurements that better link the benefits of omics and physiology.