Publications

Abstract Ocean microbes drive global-scale biogeochemical cycling 1 , but do so under constraints imposed by viruses on host community composition, metabolism, and evolutionary trajectories 2–5 . Due to sampling and cultivation challenges, genome-level viral diversity remains poorly described and grossly understudied in nature such that <1% of observed surface ocean viruses, even those that are abundant and ubiquitous, are ‘known’ 5 . Here we analyze a global map of abundant, double stranded DNA (dsDNA) viruses and viral-encoded auxiliary metabolic genes (AMGs) with genomic and ecological contexts through the Global Ocean Viromes (GOV) dataset, which includes complete genomes and large genomic fragments from both surface and deep ocean viruses sampled during the Tara Oceans and Malaspina research expeditions 6,7 . A total of 15,222 epi- and mesopelagic viral populations were identified that comprised 867 viral clusters (VCs, approximately genus-level groups 8,9 ). This roughly triples known ocean viral populations 10 , doubles known candidate bacterial and archaeal virus genera 9 , and near-completely samples epipelagic communities at both the population and VC level. Thirty-eight of the 867 VCs were identified as the most impactful dsDNA viral groups in the oceans, as these were locally or globally abundant and accounted together for nearly half of the viral populations in any GOV sample. Most of these were predicted in silico to infect dominant, ecologically relevant microbes, while two thirds of them represent newly described viruses that lacked any cultivated representative. Beyond these taxon-specific ecological observations, we identified 243 viral-encoded AMGs in GOV, only 95 of which were known. Deeper analyses of 4 of these AMGs revealed that abundant viruses directly manipulate sulfur and nitrogen cycling, and do so throughout the epipelagic ocean. Together these data provide a critically-needed organismal catalog and functional context to begin meaningfully integrating viruses into ecosystem models as key players in nutrient cycling and trophic networks.

The Mediterranean Sea ranks among the ocean regions warming fastest. There is evidence for impacts of climate change on marine Mediterranean organisms but a quantitative assessment is lacking. We compiled the impacts of warming reported in the literature to provide a quantitative assessment for the Mediterranean Sea. During the last three decades the summer surface temperature has increased 1.15 oC. Strong heat wave events have occurred in years 1994, 2003 and 2009. Impacts of warming are evident on growth, survival, fertility, migration and phenology of pelagic and benthic organisms, from phytoplankton to marine vegetation, invertebrates and vertebrates. Overall, 50 % of biological impacts in the Mediterranean Sea occur at summer surface temperature anomaly ≤ 4.5 ºC and at summer surface temperature of 27.5 ºC. The activation energy (geometric mean 1.58 ± 0.48 eV), the slope of the Arrhenius equation describing the temperature-dependence of biological processes, for the response of Mediterranean marine biota to warming reveals that these responses in the Mediterranean are far steepest than possibly explained by the direct effect of warming alone. The observations are biased toward the northern and western sectors of the basin, likely underestimating the impacts of warming in areas where warming is particularly intense.

Soils in terrestrial and coastal blue carbon ecosystems are an important carbon sink. National carbon inventories require accurate assessments of soil carbon in these ecosystems to aid conservation and nature-based climate change mitigation strategies. Here we harmonise measurements from Australia’s terrestrial and blue carbon ecosystems and apply a multiscale spatial machine learning model to estimate soil carbon stocks and drivers of variation. We find that climate and vegetation are the primary drivers of variation at the continental scale, with ecosystem type, terrain, clay content, mineralogy and nutrients drive subregional variations. We estimate that in the top 0–30cm soil layer, terrestrial ecosystems hold 27.6 Gt C (19.6–39.0 Gt C), and blue carbon ecosystems hold 0.35 GtC (0.20–0.62 GtC). Tall open eucalypt and mangrove forests have the largest soil carbon content by area, while eucalypt woodlands and hummock grasslands have the largest total carbon stock due to their large area. Our findings suggest these are important ecosystems for conservation and nature-based mitigation climate change strategies.

Significance Global vessel traffic is increasing alongside world economic growth. The potential for rising lethal ship strikes on endangered species of marine megafauna, such as the plankton-feeding whale shark, remains poorly understood since areas of highest overlap are seldom determined across an entire species range. Here we show how satellite tracking whale sharks and large vessel movements globally provides a means to localize high-overlap areas and to determine how collision risk changes in time. Our results point to potential high levels of undetected or unreported ship strikes, which may explain why whale shark populations continue to decline despite protection and low fishing-induced mortality. Collision mitigations in high-collision-risk areas appear necessary to help conserve this iconic species.

Understanding the vertical distribution of elasmobranch species and associated ecological dynamics can be a crucial component of developing effective conservation strategies, particularly in light of their global population decline. Previous studies have primarily focused on horizontal extent and movement patterns of elasmobranchs, with limited knowledge about their vertical distribution. This knowledge gap stems from limited access to technological advancements and reliance on surface data from fisheries operations. Today, advancements in observing platforms such as electronic tracking, remotely operated vehicles and submersibles, and reductions in costs for drop cameras and BRUVs, allow for direct observation of animals at great depths, facilitating improved understanding of their ecological and trophic niches. This study reports new global depth records for three elasmobranch species observed in the Saudi Arabian Red Sea ( Carcharhinus altimus , Rhinobatos punctifer, Iago omanensis ), also presenting ethological evidence on Iago omanensis feeding behavior. Our findings have significant implications for conservation strategies and the development of targeted conservation measures. The provisioning of data on new depth ranges allows places like NEOM to better manage and protect deep sea habitats, due to the presence of species occurring at those depths.

Marine macrophytes are the foundation of algal forests and seagrass meadows¬–some of the most productive and diverse coastal marine ecosystems on the planet. These ecosystems provide nursery grounds and food for fish and invertebrates, coastline protection from erosion, carbon sequestration, and nutrient fixation. For marine macrophytes, temperature is generally the most important range limiting factor, and ocean warming is considered the most severe threat among global climate change factors. ocean warming induced losses of dominant macrophytes along their equatorial range edges, as well as range extensions into polar regions, are predicted and already documented. While adaptive evolution based on genetic change is considered too slow to keep pace with the increasing rate of anthropogenic environmental changes, rapid adaptation may come about through a set of non-genetic mechanisms involving the functional composition of the associated microbiome, as well as epigenetic modification of the genome and its regulatory effect on gene expression and the activity of transposable elements. While research in terrestrial plants demonstrates that the integration of non-genetic mechanisms provide a more holistic picture of a species' evolutionary potential, research in marine systems is lagging behind. Here, we aim to review the potential of marine macrophytes to acclimatize and adapt to major climate change effects via intraspecific variation at the genetic, epigenetic, and microbiome levels. All three levels create phenotypic variation that may either enhance fitness within individuals (plasticity) or be subject to selection and ultimately, adaptation. We review three of the most important phenotypic variations in a climate change context, including physiological variation, variation in propagation success, and in herbivore resistance. Integrating different levels of plasticity, and adaptability into ecological models will allow to obtain a more holistic understanding of trait variation and a realistic assessment of the future performance and distribution of marine macrophytes. Such multi-disciplinary approach that integrates various levels of intraspecific variation, and their effect on phenotypic and physiological variation, is of crucial importance for the effective management and conservation of seagrasses and macroalgae under climate change.

Abstract. Mangrove forests are highly productive tropical and subtropical coastal systems that provide a variety of ecosystem services, including the sequestration of carbon. While mangroves are reported to be the most intense carbon sinks among all forests, their sediments can also support large emissions of greenhouse gases (GHG), such as carbon dioxide (CO2) and methane (CH4), to the atmosphere. However, data derived from arid mangrove systems like the Red Sea are lacking. Here, we report emission rates of CO2 and CH4 from mangrove sediments along the Saudi Arabian coast of the Red Sea, and assess the relative role of these two gases in supporting total GHG emissions. Diel CO2 and CH4 emission rates in Red Sea mangrove sediments ranged from −3452 to 7500 µmol CO2 m−2 d−1 and from 0.9 to 13.3 µmol CH4 m−2 d−1, respectively. The rates reported here fall within previously reported ranges for both CO2 and CH4, but maximum CO2 and CH4 flux rates in the Red Sea are 10 to 100-fold below those previously reported for mangroves elsewhere. Based on the isotopic composition of the CO2 and CH4 produced by mangrove sediments, we identified the origin of the organic matter that supports GHG emissions. In most of the mangrove stands, GHG emissions were supported by organic matter from mixed sources while only in one mangrove stand the GHG emissions were supported by organic matter derived from mangrove tissues. Moreover, the organic matter derived from mangrove tissues reduced CO2 fluxes and enhanced CH4 production, pointing out the importance of the origin of the organic matter in GHG emissions. Methane was the main source of CO2-equivalents, despite the comparatively low emission rates, in most of the sampled mangroves, and therefore deserves careful monitoring in this region. Despite the mean net emission of CO2 and CH4 by Red Sea mangroves reported here, these forests become net organic carbon sinks when taking into account the existing carbon burial rates for the Red Sea mangroves. By further resolving GHG fluxes in arid mangroves, we will better ascertain the role of these forests in global carbon budgets.