Proteogenomics for Non-model Ocean-Derived Fungi.

Most biological and biomedical experiments are designed and studied using the most common model organisms (MOs) like humans, mice, Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, worms, fruit flies, zebrafish, and Arabidopsis thaliana. These model organisms have been extensively studied and have a well-established set of genetic, physiological, and other tools available for research. In contrast, non-model organisms (NMOs) are those that are not traditionally used in scientific research and do not have a well-established set of genetic or other biological tools available for their study. The majority of MOs are associated with land habitats but rarely with ocean environments. The ocean forms the largest portion of our planet, yet ocean-derived organisms are the least explored, and these organisms are primarily NMOs. However, these are thrilling living entities, such as ocean-derived fungi (ODF). These ODFs are a diverse group of fungi that live in different ocean sectors, including the ocean, estuaries, and coastal ecosystems. These fungi are found to colonize and adapt to different substrates. They are important decomposers in marine ecosystems, breaking down dead organic matter and recycling nutrients. ODFs have adapted to survive in the unique and challenging conditions of the ocean environment, including high salt concentrations, low nutrient availability, and exposure to waves and currents. ODFs are potent producers of natural compounds with pharmaceutical and industrial applications, such as antibiotics, anticancer agents, antivirals, and enzymes for industrial processes. ODFs are an exciting group of fungi; however, these are the least studied because of the nonavailability of MOs from this group. Hence, there is a massive scope of expanding our current knowledge about ODFs, their genetic traits, potential future drug-producing capabilities, and lifestyle traits.With the advent of next-generation DNA sequencing, there is huge potential for the characterization of the genetic material of ODF as NMOs. Parallel proteomic methods also pose huge potential. A marriage of NGS and proteomic methods generates a new avenue called proteogenomics, which focuses on better annotation of existing genomic data. Both methods are getting cheaper and accessible to the research community for studying the proteogenomics of NMOs. Herein, the proteogenomic protocol development and data analyses are illustrated for the ocean-derived fungus Scopulariopsis brevicaulis.

Deep-ocean macrofaunal assemblages on ferromanganese and phosphorite-rich substrates in the Southern California Borderland.

Mineral-rich hardgrounds, such as ferromanganese (FeMn) crusts and phosphorites, occur on seamounts and continental margins, gaining attention for their resource potential due to their enrichment in valuable metals in some regions. This study focuses on the Southern California Borderland (SCB), an area characterized by uneven and heterogeneous topography featuring FeMn crusts, phosphorites, basalt, and sedimentary rocks that occur at varying depths and are exposed to a range of oxygen concentrations. Due to its heterogeneity, this region serves as an optimal setting for investigating the relationship between mineral-rich hardgrounds and benthic fauna. This study characterizes the density, diversity, and community composition of macrofauna (>300 µm) on hardgrounds as a function of substrate type and environment (depth and oxygen ranges). Rocks and their macrofauna were sampled quantitatively using remotely operated vehicles (ROVs) during expeditions in 2020 and 2021 at depths above, within, and below the oxygen minimum zone (OMZ). A total of 3,555 macrofauna individuals were counted and 416 different morphospecies (excluding encrusting bryozoans and hydrozoans) were identified from 82 rocks at depths between 231 and 2,688 m. Average density for SCB macrofauna was 11.08 ± 0.87 ind. 200 cm-2 and mean Shannon-Wiener diversity per rock (H'[loge]) was 2.22 ± 0.07. A relationship was found between substrate type and macrofaunal communities. Phosphorite rocks had the highest H' of the four substrates compared on a per-rock basis. However, when samples were pooled by substrate, FeMn crusts had the highest H' and rarefaction diversity. Of all the environmental variables examined, water depth explained the largest variance in macrofaunal community composition. Macrofaunal density and diversity values were similar at sites within and outside the OMZ. This study is the first to analyze the macrofaunal communities of mineral-rich hardgrounds in the SCB, which support deep-ocean biodiversity by acting as specialized substrates for macrofaunal communities. Understanding the intricate relationships between macrofaunal assemblages and mineral-rich substrates may inform effects from environmental disruptions associated with deep-seabed mining or climate change. The findings contribute baseline information useful for effective conservation and management of the SCB and will support scientists in monitoring changes in these communities due to environmental disturbance or human impact in the future.

The calculated voyage: benchmarking optimal strategies and consumptions in the Japanese eel's spawning migration.

Eels migrate along largely unknown routes to their spawning ground. By coupling Zermelo's navigation solution and data from the Japan Coastal Ocean Predictability Experiment 2 (JCOPE2M), we simulated a range of seasonal scenarios, swimming speeds, and swimming depths to predict paths that minimize migration duration and energy cost. Our simulations predict a trade-off between migration duration and energy cost. Given that eels do not refuel during their migration, our simulations suggest eels should travel at speeds of 0.4-0.6 body-length per second to retain enough energy reserves for reproduction. For real eels without full information of the ocean currents, they cannot optimize their migration in strong surface currents, thus when swimming at slow swimming speeds, they should swim at depths of 200 m or greater. Eels swimming near the surface are also influenced by seasonal factors, however, migrating at greater depths mitigates these effects. While greater depths present more favorable flow conditions, water temperature may become increasingly unfavorable, dropping near or below 5 °C. Our results serve as a benchmark, demonstrating the complex interplay between swimming speed, depth, seasonal factors, migration time, and energy consumption, to comprehend the migratory behaviors of Japanese eels and other migratory fish.

Parasitic taxa are key to the vertical stratification and community variation of pelagic ciliates from the surface to the abyssopelagic zone.

BACKGROUND: An increase in upper-ocean thermal stratification is being observed worldwide due to global warming. However, how ocean stratification affects the vertical profile of plankton communities remains unclear. Understanding this is crucial for assessing the broader implications of ocean stratification. Pelagic ciliates cover multiple functional groups, and thus can serve as a model for studying the vertical distribution and functional strategies of plankton in stratified oceans. We hypothesize that pelagic ciliate communities exhibit vertical stratification caused by shifts in functional strategies, from free-living groups in the photic zone to parasitic groups in deeper waters. RESULTS: 306 samples from the surface to the abyssopelagic zone were collected from 31 stations in the western Pacific and analyzed with environmental DNA (the V4 region of 18 S rDNA) metabarcoding of pelagic ciliates. We found a distinct vertical stratification of the entire ciliate communities, with a boundary at a depth of 200 m. Significant distance-decay patterns were found in the photic layers of 5 m to the deep chlorophyll maximum and in the 2,000 m, 3000 m and bottom layers, while no significant pattern occurred in the mesopelagic layers of 200 m - 1,000 m. Below 200 m, parasitic Oligohymenophorea and Colpodea became more prevalent. A linear model showed that parasitic taxa were the main groups causing community variation along the water column. With increasing depth below 200 m, the ASV and sequence proportions of parasitic taxa increased. Statistical analyses indicated that water temperature shaped the photic communities, while parasitic taxa had a significant influence on the aphotic communities below 200 m. CONCLUSIONS: This study provides new insights into oceanic vertical distribution, connectivity and stratification from a biological perspective. The observed shift of functional strategies from free-living to parasitic groups at a 200 m transition layer improves our understanding of ocean ecosystems in the context of global warming.

Remote science at sea with remotely operated vehicles.

Conducting sea-going ocean science no longer needs to be limited to the number of berths on a ship given that telecommunications, computing, and networking technologies onboard ships have become familiar mechanisms for expanding scientists' reach from onshore. The oceanographic community routinely works with remotely operated vehicles (ROVs) and pilots to access real-time video and data from the deep sea, while onboard a ship. The extension of using an ROV and its host vessel's live-streaming capabilities has been popularized for almost 3 decades as a telepresence technology. Telepresence-enabled vessels with ROVs have been employed for science, education, and outreach, giving a greater number of communities viewing access to ocean science. However, the slower development of technologies and social processes enabling sustained real-time involvement between scientists on-ship and onshore undermines the potential for broader access, which limits the possibility of increasing inclusivity and discoveries through a diversity of knowledge and capabilities. This article reviews ocean scientists' use of telepresence for ROV-based deep-sea research and funded studies of telepresence capabilities. The authors summarize these studies findings and conditions that lead to defining the use of telepresence-enabled vessels for "remote science at sea." Authors define remote science at sea as a type of ocean expedition, an additional capability, not a replacement for all practices by which scientists conduct ocean research. Remote science for ocean research is an expedition at-sea directed by a distributed science team working together from at least two locations (on-ship and onshore) to complete their science objectives for which primary data is acquired by robotic technologies, with connectivity supported by a high-bandwidth satellite and the telepresence-enabled ship's technologies to support the science team actively engaged before, during, and after dives across worksites. The growth of productive ocean expeditions with remote science is met with social, technical, and logistical challenges that impede the ability of remote scientists to succeed. In this article, authors review telepresence-enabled ocean science, define and situate the adjoined model of remote science at sea, and some infrastructural, technological and social considerations for conducting and further developing remote science at sea.

The role of larval transport on recruitment dynamics of red mullet (Mullus barbatus) in the Central Mediterranean Sea.

Recruitment success depends on external forcing mechanisms such as ocean currents that affect the transport of eggs and larvae to favorable habitats. In this study, we investigated the role of larval transport in the recruitment of Mullus barbatus in the Central Mediterranean Sea by modeling the recruits' abundance as a function of both spawning stock size and dispersal rates of the species' early life stages. Our analysis involved twenty years of data on recruits and spawners abundance obtained from scientific trawl surveys, and data on larval dispersal rates derived from a combination of actualized published sources and original data. By calculating the estimates of retention, import and uniformity of the contribution of the spawning areas distributed among different Geographical Sub Areas (GSAs) in the Sicilian nurseries, we assessed their contribution to recruitment using modified Ricker stock size-recruits models. In particular, our results show that a high uniform contribution from spawning areas within GSA16, mainly related to the oceanographic patterns promoting larval retention, together with spawners abundance, significantly reduced the variability of red mullet recruitment. We further highlighted that when switching from a higher to a lower level of evenness of contribution to the recruit population from different spawning areas in the GSA16, the expected spawning stock abundance per recruit for a given fishing pattern can suffer a rapid short-term decline, which is likely to have negative consequences for stock assessment and management decisions. Our results suggest that larval transport plays a crucial role in explaining the interannual variability of recruitment, thereby contributing to a better understanding of stock size variation. Additionally, our study enhances the understanding of the spatial dynamics involved in the recruitment of this species, which is of increasing interest within fisheries management frameworks.

Effects of single or combined exposure to tralopyril and ocean acidification on energy metabolism response and sex development in Pacific oysters (Crassostrea gigas).

The combined effects of the novel antifouling biocide tralopyril (TP) nitrile and ocean acidification (OA) on marine organisms are still not well understood, despite the increasing attention given to the toxic effects of emerging pollutants and OA on marine organisms in recent years. In this study, Crassostrea gigas (C. gigas) was exposed to TP, OA, and a combination of TP and OA for 21 days with a 14-day depuration. This study investigated the inter-tissue variability in energy metabolism responses and the impacts on gonadal development in C. gigas under both single and combined exposures to TP and OA. The results indicate that TP exposure and OA resulted in up-regulation of energy metabolism genes in the C. gigas, with tissues exhibiting enhanced aerobic metabolism. Furthermore, OA influences the sex determination of C. gigas, promoting the development of female individuals. Moreover, following depuration, C. gigas is able to restore normal energy metabolism and sexual development through the accumulation of suitable energy reserves. This study provides a valuable reference for the environmental and ecological risk assessment of TP, addressing the research gap in understanding the combined toxicity of TP and OA on aquatic organisms.

Strong winds reduce foraging success in albatrosses.

Knowledge of how animals respond to weather and changes in their physical environment is increasingly important, given the higher frequency of extreme weather recorded in recent years and its forecasted increase globally.1,2 Even species considered to be highly adapted to extremes of weather, as albatrosses are to strong winds,3,4,5 may be disadvantaged by shifts in those extremes. Tracked albatrosses were shown recently to avoid storms and the strongest associated winds.6 The drivers of this response are so far unknown, though we hypothesize that turbulent storm conditions restrict foraging success, possibly by reducing the detectability or accessibility of food, and albatrosses divert toward more profitable conditions where possible. We tested the impact of the physical environment-wind speed, rainfall, water clarity, and time of day-on feeding activity and success of two species of albatrosses with contrasting foraging strategies. We tracked 33 wandering and 48 black-browed albatrosses from Bird Island (South Georgia) with GPS and immersion loggers, and 19 and 7 individuals, respectively, with stomach-temperature loggers to record ingestions, providing an in-depth picture of foraging behavior. Reduced foraging profitability (probability of prey capture and overall mass) was associated with stormy conditions, specifically strong winds and heavy rain in surface-seizing wandering albatrosses, and the probability of prey capture was reduced in strong winds in black-browed albatrosses. We show that even highly wind-adapted species may frequently encounter conditions that make foraging difficult, giving context to storm avoidance in albatrosses.

Warming and UV Radiation Alleviate the Effect of Virus Infection on the Microalga Emiliania huxleyi.

The marine microalga Emiliania huxleyi is widely distributed in the surface oceans and is prone to infection by coccolithoviruses that can terminate its blooms. However, little is known about how global change factors like solar UV radiation (UVR) and ocean warming affect the host-virus interaction. We grew the microalga at 2 temperature levels with or without the virus in the presence or absence of UVR and investigated the physiological and transcriptional responses. We showed that viral infection noticeably reduced photosynthesis and growth of the alga but was less harmful to its physiology under conditions where UVR influenced viral DNA expression. In the virus-infected cells, the combination of UVR and warming (+4°C) led to a 13-fold increase in photosynthetic carbon fixation rate, with warming alone contributing a change of about 5-7-fold. This was attributed to upregulated expression of genes related to carboxylation and light-harvesting proteins under the influence of UVR, and to warming-reduced infectivity. In the absence of UVR, viral infection downregulated the metabolic pathways of photosynthesis and fatty acid degradation. Our results suggest that solar UV exposure in a warming ocean can reduce the severity of viral attack on this ecologically important microalga, potentially prolonging its blooms.

Nature-based solutions to the management of legacy plastic pollution: Filter-feeders as bioremediation tools for coastal microplastics.

Plastics are one of the most topical pollutants occurring in our ocean. Given concern regarding the impacts of both macro- and micro-plastics on environmental and human well-being, a range of management approaches are required. Key in the management of microplastics will be curative measures that facilitate the removal of legacy plastics from the environment as, without their removal, impacts will continue for centuries. While a strong focus has been placed on technical, engineered solutions to plastic removal, many of these techniques are unsuitable for microplastics. Therefore, here we argue for the exploration of nature-based solutions to such issues. As a case study, we combine information available in the published academic literature with experimental results from a pilot study to highlight the potential for filter-feeding organisms - specifically mussels - to remove microplastics from the water column by transferring them into biodeposits. Such biodeposits have the potential to be transported to other parts of the system (i.e., benthic regions), or collected and removed from the environment. While initial results indicate that such approaches are promising for microplastic removal from water sources, there are a number of areas that still need investigation before widespread application of such an approach could be adopted. Key knowledge gaps include identification of the appropriate methods to be used and assessment of unintended consequences including potential impacts of microplastics on benthic organisms. We argue that there is a need for ongoing funding and policy support for the development and application of such nature-based solutions targeting legacy plastic pollution.

Coral Community Composition Linked to Hypoxia Exposure.

Tropical reef ecosystems are strongly influenced by the composition of coral species, but the factors influencing coral diversity and distributions are not fully understood. Here we demonstrate that large variations in the relative abundance of three major coral species across adjacent Caribbean reef sites are strongly related to their different low O2 tolerances. In laboratory experiments designed to mimic reef conditions, the cumulative effect of repeated nightly low O2 drove coral bleaching and mortality, with limited modulation by temperature. After four nights of repeated low O2, species responses also varied widely, from > 50% bleaching in Acropora cervicornis to no discernable sensitivity of Porites furcata. A simple metric of hypoxic pressure that combines these experimentally derived species sensitivities with high-resolution field data accurately predicts the observed relative abundance of species across three reefs. Only the well-oxygenated reef supported the framework-building hypoxia-sensitive Acropora cervicornis, while the hypoxia-tolerant weedy species Porites furcata was dominant on the most frequently O2-deplete reef. Physiological exclusion of acroporids from these O2-deplete reefs underscores the need for hypoxia management to reduce extirpation risk.

Vertical heterogeneity enhances network complexity and stability of co-occurrence microbes in the eastern Indian Ocean.

Microbes are core to driving biogeochemical cycles and differ between sun-drenched surface and relatively dark deep oceans. However, their distinct contributions to the organization and association of communities are still remaining elusive. Here, their assembly and co-occurrence stability are systematically researched along the surface and vertical gradients in the eastern Indian Ocean. The distribution of surface microbes was grouped tightly with closer phylogenetic distance and broader niche breadth, and separately from those vertical samples. Clear distance-decay of community similarity was observed in surface microbes with lower richness, while more diverse microeukaryotes and prokaryotes were observed in surface and vertical environments, respectively. Co-occurrence microbes along vertical gradients had a more complex network that was dominated by prokaryotes, while exhibited a lower modularity compared to the surface network. Microbial associations along vertical gradients were more stable and resilient, with lower robustness, higher vulnerability, and a relatively consistent fragmentation. Moreover, prokaryotes contribute greatly to the network topology and stability compared to microeukaryotes in surface environments, emphasizing their distinct functions and survival strategies in maintaining community stability across spatial variations. Environmental selection and community differentiation led to the divergence in organization and potential function of microbes. This study shed light on new perspectives on how marine microbes were associated with and influenced by spatial heterogeneity and their distinct roles in community organization in the face of environmental fluctuations.

The Escalating threat of climate change-driven diseases in fish: Evidence from a global perspective - A literature review.

Climate change has brought significant alterations to the aquatic environment, leading to the rapid spread of infectious fish diseases with increasing water temperatures. It is crucial to understand how aquatic pathogens will impact fish in the context of climate change. This study aimed to assess the effects of climate change on fish diseases globally. Data from 104 papers published between 2003 and 2022 were analyzed to identify recent trends in the field. The majority of the studies (54%) focused on parasites, particularly proliferative kidney disease, while 22% examined bacteria. The United States accounted for 19% of the studies, followed by Canada at 14%, covering a wide range of fish species. More research was published on farmed fish (54%) than wild fish (30%), with a higher emphasis on freshwater species (62%) compared to marine species (34%). Most published studies (64%) focused on the local environment rather than the farm level (7%). The findings highlight temperature as a significant threat to global aquaculture and fisheries, impacting the progression of fish diseases. These impacts could be exacerbated by factors such as pH, salinity, and ocean acidification, posing challenges to fish health. Therefore, there is a pressing need for enhanced research and management strategies to address these issues effectively in the future.

Drivers of summer Arctic sea-ice extent at interannual time scale in CMIP6 large ensembles revealed by information flow.

Arctic sea-ice extent has strongly decreased since the beginning of satellite observations in the late 1970s. While several drivers are known to be implicated, their respective contribution is not fully understood. Here, we apply the Liang-Kleeman information flow method to five different large ensembles from the Coupled Model Intercomparison Project Phase 6 (CMIP6) over the 1970-2060 period to investigate the extent to which fluctuations in winter sea-ice volume, air temperature and ocean heat transport drive changes in subsequent summer Arctic sea-ice extent. This allows us to go beyond classical correlation analyses. Results show that air temperature is the most important controlling factor of summer sea-ice extent at interannual time scale, and that winter sea-ice volume and Atlantic Ocean heat transport play a secondary role. If we replace air temperature by net shortwave and downward longwave radiations, we find that the sum of influences from both radiations is almost similar to the air temperature influence, with the longwave radiation being dominant in driving changes in summer sea-ice extent. Finally, we find that the influence of air temperature is more prominent during periods of large sea-ice reduction and that this temperature influence has overall increased since 1970.

Effects of recent urbanization on carbon and nitrogen burial rates of sedimentary records in a tropical coastal lagoon (Brazil).

Land use and land cover changes (LULCC) are a global environmental issue that has impacted biogeochemical cycles worldwide. Sedimentary records can demonstrate the effects of LULCC on aquatic ecosystems, where the recent urbanization has been linked to changes in carbon and nitrogen burial. In this study, we reconstructed long-term LULCC and sedimentary records of carbon (C), nitrogen (N), phosphorus (P), and sediment burial rates in a eutrophic tropical coastal lagoon affected by recent urban expansion. Based on analyses of 30 years of satellite imagery and sedimentary records from 1932 to 2013, we revealed that urban expansion over low-productivity agricultural-pasture areas increased siltation and C, N, P concentrations and fluxes in the coastal lagoon. Large temporal variability of such parameters revealed not only the effects of LULCC on the lagoon's burial rates, but also the influence of artificial sand barrier openings, which connect the studied lagoon to the sea, reducing C, N, P, and particle deposition in the sediment. Our results support multi-proxy methods to assess the relationships between recent urbanization, rising C, N, and P burial rates, and the eutrophication process. We highlight that artificial sandbar openings, the current eutrophication management strategy for coastal lagoons, are ineffective in reducing the eutrophication state, even in the recent scenario of decreasing C, N, and P burial rates.

Description of three new species of Kudoa Meglitsch, 1947 (Myxozoa: Multivalvulida) in commercial marine fishes from southern China, and new host records.

Multivalvulidan myxosporeans (Multivalvulida) of the genera Unicapsula Davis, 1924 and Kudoa Meglitsch, 1947 are mostly causative agents of latent and imperceptible infection in marine fishes. However, they are sometimes incriminated in causing post-mortem myoliquefaction or unsightly cyst formation in commercial fish. Despite the great commercial impacts of multivalvulidan infection, the biodiversity, host range and epidemiology of multivalvulidan species remain to be explored further, including infection of alternative annelid hosts. Therefore, this study aimed to identify multivalvulidan species and their host and/or distribution records in commercial fishes in China. Multivalvulidan infection was detected in ten commercial fish species of seven families from the South and East China Seas (Northwest Pacific Ocean) and the Eastern Central Atlantic Ocean (an imported Dagetichthys lusitanicus [de Brito Capello]). Based on morphological and molecular-genetic analyses of their small and large subunit of ribosomal RNA genes, five new host and/or geographical distribution records for five fish species are presented, and three new species in five fish species are described, namely Kudoa neoscomberomori sp. n. in Scomberomorus commerson (Lacépède); Kudoa pilosa sp. n. in Helicolenus hilgendorfi (Döderlein) (type host) and Sebastiscus tertius (Barsukov et Chen); and Kudoa tumidisporica sp. n. in Photopectoralis bindus (Valenciennes) (type host) and Nuchequula nuchalis (Temminck et Schlegel). This study provides new data on multivalvulidan diversity in the ocean ecosystem.

Regulation of terrestrial input and ocean processes on the occurrence and transport of traditional and emerging per- and polyfluoroalkyl substances in the inner shelf of the East China Sea.

Coastal oceans, serving as transitional zones between land and sea, possess unique geographical features and complex hydrological conditions, functioning as regional reservoirs and crucial transport pathways for anthropogenic pollutants such as per- and polyfluoroalkyl substances (PFASs) to the open ocean. This study comprehensively investigates traditional perfluoroalkyl carboxylic and sulphonic acids (PFCAs and PFSAs) and emerging perfluoroalkyl ether carboxylic and sulfonic acids (PFECAs and PFESAs), fluorotelomer sulfonates (FTSAs) in seawater columns and surface sediments from the inner shelf of the East China Sea, by integrating hydrological and biogeochemical data. Comparable levels of traditional and emerging PFASs were observed in seawater samples, in contrast to higher concentrations of traditional PFASs in surface sediments. Waterborne PFASs exhibited a nearshore-to-offshore decreasing trend and a surface enrichment pattern in offshore waters, typically influenced by terrestrial inputs and oceanic processes. Significant terrestrial inputs for waterborne PFASs were identified, including large rivers like the Changjiang River (Yangtze) and semi-enclosed coastal bays such as Xiangshan Port and Sanmen Bay, where prolonged hydraulic retention times contribute to PFAS accumulation. The source apportionment model demonstrated that emerging fluorochemical manufacturing, textile production, and high-performance fluoropolymer materials are primary sources, consistent with PFAS releases from commercial products and industrial processes along the Changjiang River and in Xiangshan County. Hydrologically, the offshore transport barrier effect created by river plume fronts, and the vertical stratification of different water masses were significant for PFASs. Sediment inputs and resuspension also played a crucial role, with surface sediment-bottom water partitioning behavior primarily regulated by the hydrophobicity of PFASs and salting-out effects. While the overall ecological risks of PFASs were low, elevated risks associated with legacy perfluorooctanoate (PFOA), perfluorooctane sulfonate (PFOS), and emerging hexafluoropropylene oxide dimer acid (HFPO-DA) warrant closer attention due to their accumulation in the environment. The methodologies and findings of this research provide valuable insights into PFAS cycling in coastal oceans worldwide.

Deep-sea ecosystems of the Indian Ocean >1000 m.

The Indian Ocean is the third largest of the world's oceans, accounting for ~20 % for the global marine realm. It is geomorphologically complex, hosting a wide variety of ecosystems across basins, trenches, seamounts, ridges, and fracture zones. While modern exploration has contributed significantly to our knowledge of its coastal ecosystems, deeper waters (>1000 m) remain relatively unknown despite accounting for over 90 % of its total area. This study provides the first comprehensive review of the Indian Ocean's diverse deep sea, presenting ecosystem knowledge summaries for each major seafloor feature, contextualised with the broader historical, socioeconomic, geological, and oceanographic conditions. Unsurprisingly, some ecosystems are better characterised than others, from the relatively well-surveyed Java (Sunda) Trench and hydrothermal vents of the Carlsberg, Central and Southwest Indian Ridges, to the unexplored Southeast Indian Ridge and hadal features of the western Indian Ocean. Similarly, there is a large depth discrepancy in available records with a clear bias towards shallower sampling. We identify four outstanding problems to be addressed for the advancement of deep-sea research in the Indian Ocean: 1) inconsistencies in research extent and effort over spatial scales, 2) severe lack of data over temporal scales, 3) unexplored deep pelagic environments, and 4) a need to place the Indian Ocean's deep-sea ecosystems in a global context. By synthesising and championing existing research, identifying knowledge gaps, and presenting the outstanding problems to be addressed, this review provides a platform to ensure this forgotten ocean is prioritised for deep-sea research during the UN Ocean Decade and beyond.

Contrasting species-specific stress response to environmental pH determines the fate of coccolithophores in future oceans.

Molecular mechanisms driving species-specific environmental sensitivity in coccolithophores are unclear but crucial in understanding species selection and adaptation to environmental change. This study examined proteomic and physiological changes in three species under varying pH conditions. We showed that changing pH drives intracellular oxidative stress and changes membrane potential. Upregulation in antioxidant, DNA repair and cell cycle-related protein-groups indicated oxidative damage across high (pH 8.8) and low pH (pH 7.6) compared to control pH (pH 8.2), and correlated with reduced growth rates. Upregulation of mitochondrial proteins suggested higher metabolite demand for restoring cellular homeostasis under pH-induced stress. Photosynthetic rates generally correlated with CO2 availability, driving higher net carbon fixation rates at low pH. The intracellular pH-buffering capacity of the coastal Chrysotila carterae and high metabolic adaptability in the bloom-forming Gephyrocapsa huxleyi will likely facilitate their adaptation to ocean acidification or artificial ocean alkalinisation. However, the pH sensitivity of the ancient open-ocean Coccolithus braarudii will possibly result in reduced growth and shrinking of its ecological niche.