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Abstract Coral bleaching events from thermal stress are increasing globally in duration, frequency, and intensity. While bleaching can cause mortality, some corals survive, reacquire symbionts, and recover. We experimentally bleachedMontipora capitatato examine molecular and physiological differences between corals that recover (resilient) and those that die (susceptible). Corals were collected and monitored for eight months post-bleaching to identify genets with long-term resilience. Using an integrated systems-biology approach that included quantitative proteomics, 16S rRNA sequencing to characterize the coral microbiome, total coral lipids, symbiont community composition and density, we explored molecular-level mechanisms of tolerance in corals pre- and post-bleaching. Prior to thermal stress, resilient corals have a more diverse microbiome and abundant proteins essential for carbon acquisition, symbiont retention, and pathogen resistance. Protein signatures of susceptible corals showed early symbiont rejection and utilized urea for carbon and nitrogen. Our results reveal molecular factors for surviving bleaching events and identify diagnostic protein biomarkers for reef management and restoration. 

Since the discovery of perchlorates in martian soils, astrobiologists have been curious if and how life could survive in these low-water, high-salt environments. Perchlorates induce chaotropic and oxidative stress but can also confer increased cold tolerance in some extremophiles. Though bacterial survival has been demonstrated at subzero temperatures and in perchlorate solution, proteomic analysis of cells growing in an environment like martian regolith brines-perchlorate with subzero temperatures-has yet to be demonstrated. By defining biosignatures of survival and growth in perchlorate-amended media at subzero conditions, we move closer to understanding the mechanisms that underlie the feasibility of life on Mars. Colwellia psychrerythraea str. 34H (Cp34H), a marine psychrophile, was exposed to perchlorate ions in the form of a diluted Phoenix Mars Lander Wet Chemistry Laboratory solution at -1°C and -5°C. At both temperatures in perchlorate-amended media, Cp34H grew at reduced rates. Mass spectrometry-based proteomics analyses revealed that proteins responsible for mitigating effects of oxidative and chaotropic stress increased, while cellular transport proteins decreased. Cumulative protein signatures suggested modifications to cell-cell or cell-surface adhesion properties. These physical and biochemical traits could serve as putative identifiable biosignatures for life detection in martian environments. 

Abstract Data-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use of in silico generated spectral libraries. However, the generation of high-quality spectral libraries for DIA data analysis remains a challenge, particularly because most such libraries are generated directly from data-dependent acquisition (DDA) data or are from in silico prediction using models trained on DDA data. In this study, we introduce Carafe, a tool that generates high-quality experiment-specific in silico spectral libraries by training deep learning models directly on DIA data. We demonstrate the performance of Carafe on a wide range of DIA datasets, where we observe improved fragment ion intensity prediction and peptide detection relative to existing pretrained DDA models. To make Carafe more accessible to the community, we integrate Carafe into the widely used Skyline tool. 

Aqueous-soluble hydrocarbons dissolve into the ocean’s interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partially partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning of two free-living Cycloclasticus strains recovered from seawater incubations with n-pentane and distinguish them as an open ocean variant and a seep-proximal variant, each with distinct capabilities for hydrocarbon catabolism. Comparative metagenomic analysis indicates the variant more frequently observed further from natural seeps encodes more general pathways for hydrocarbon consumption, including short-chain alkanes, aromatics, and long-chain alkanes, and also possesses redox versatility in the form of respiratory nitrate reduction and thiosulfate oxidation; in contrast, the seep variant specializes in short-chain alkanes and relies strictly on oxygen as the terminal electron acceptor. Both variants observed in our work were dominant ecotypes of Cycloclasticus observed during the Deepwater Horizon disaster, a conclusion supported by 16S rRNA gene analysis and read-recruitment of sequences collected from the submerged oil plume during active flow. A comparative genomic analysis of Cycloclasticus across various ecosystems suggests distinct strategies for hydrocarbon transformations among each clade. Our findings suggest Cycloclasticus is a versatile and opportunistic consumer of hydrocarbons and may have a greater role in the cycling of sulfur and nitrogen, thus contributing broad ecological impact to various ecosystems globally. 

ABSTRACT Teleost fishes are a highly diverse, ecologically essential group of aquatic vertebrates that include coho salmon (Oncorhynchus kisutch). Coho are semelparous and all ovarian follicles develop synchronously. Owing to their ubiquitous distribution, teleosts provide critical sources of food worldwide through subsistence, commercial fisheries, and aquaculture. Enhancement of hatchery practices requires 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 have described a coho salmon ovarian proteome of over 5700 proteins, generated with data independent acquisition, revealing the proteins that change through the transition from primary to secondary ovarian follicle development. This transition is critical during the onset of puberty and for determining egg quality and embryonic development. Primary follicle development was marked by differential abundances of proteins in carbohydrate metabolism, protein turnover, and the complement pathway, suggesting elevated metabolism as the follicles develop through stages of oogenesis. 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. 

Diel rhythms are observed across taxa and are important for maintaining synchrony between the environment and organismal physiology. A striking example of this is the diel vertical migration undertaken by zooplankton, some of which, such as the 5 mm-long copepod Pleuromamma xiphias (P. xiphias), migrate hundreds of meters daily between the surface ocean and deeper waters. Some of the molecular pathways that underlie the expressed phenotype at different stages of this migration are entrained by environmental variables (e.g., day length and food availability), while others are regulated by internal clocks. We identified a series of proteomic biomarkers that vary across ocean DVM and applied them to copepods incubated in 24 h of darkness to assess circadian control. The dark-incubated copepods shared some proteomic similarities to the ocean-caught copepods (i.e., increased abundance of carbohydrate metabolism proteins at night). Shipboard-incubated copepods demonstrated a clearer distinction between night and day proteomic profiles, and more proteins were differentially abundant than in the in situ copepods, even in the absence of the photoperiod and other environmental cues. This pattern suggests that there is a canalization of rhythmic diel physiology in P. xiphias that reflects likely circadian clock control over diverse molecular pathways. 

The persistence of coral reefs requires the survival of adult coral colonies and their continued sexual reproduction despite thermal stress. To assess the trophic pathway (i.e., autotrophy and/or heterotrophy) used to develop gametes following bleaching, we thermally stressedMontipora capitatafor one month at a time when corals in Hawai’i typically experience elevated seawater temperatures. After six and nine months of recovery, we pulse-chased non-bleached and previously bleached colonies using a dual-label design to compare the allocation of carbon and nitrogen at significant stages of gamete development. Dissolved inorganic carbon- (DI¹³C) and nitrogen- (DI¹⁵N) labelled seawater or¹³C- and¹⁵N-labelled rotifers were used to assess the autotrophic and heterotrophic pathways, respectively. At multiple time points for up to two years later, we collected adult coral fragments and isolated host tissue, Symbiodiniaceae cells, and developing eggs and captured gamete bundles to analyze their carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotopes. We found that the presence of Symbiodiniaceae was important for gametogenesis in both non-bleached and previously bleached colonies in two main ways. First, autotrophically-acquired carbon and nitrogen were both allocated to gametes during development, suggesting that recovery of photosynthesis after bleaching is critical for gametogenesis. Second, only heterotrophically-acquired nitrogen, not carbon, was incorporated into gametes and was readily recycled between host tissues and Symbiodiniaceae cells. This suggests that one of the purposes of heterotrophy following coral bleaching forM. capitatamay be to supplement the nitrogen pool, providing available nutrients for endosymbiotic algal growth. Allocation of carbon and nitrogen to eggs coincided with the period when vertical transmission of symbionts to gametes occurs, further supporting the important relationship between gametogenesis and availability of Symbiodiniaceae forM. capitata. 

Abstract Diatoms are important primary producers in the world's oceans, yet their growth is constrained in large regions by low bioavailable iron (Fe). Low‐Fe stress‐induced limitation of primary production is due to requirements for Fe in components of essential metabolic pathways including photosynthesis and other chloroplast plastid functions. Studies have shown that under low‐Fe stress, diatoms alter plastid‐specific processes, including components of electron transport. These physiological changes suggest changes of protein content and in protein abundances within the diatom plastid. While in silico predictions provide putative information on plastid‐localized proteins, knowledge of diatom plastid proteins remains limited in comparison to well‐studied model photosynthetic organisms. To address this, we employed shotgun proteomics to investigate the proteome of subcellular plastid‐enriched fractions fromThalassiosira pseudonanato gain a better understanding of how the plastid proteome is remodeled in response to Fe limitation. Using mass spectrometry‐based peptide identification and quantification, we analyzedT. pseudonanagrown under Fe‐replete and ‐limiting conditions. Through these analyses, we inferred the relative quantities of each protein, revealing that Fe limitation regulates major metabolic pathways in the plastid, including the Calvin cycle. Additionally, we observed changes in the expression of light‐harvesting proteins. In silico localization predictions of proteins identified in this plastid‐enriched proteome allowed for an in‐depth comparison of theoretical versus observed plastid‐localization, providing evidence for the potential of additional protein import pathways into the diatom plastid.