Distinguishing the molecular diversity, nutrient content, and energetic potential of exometabolomes produced by macroalgae and reef-building corals.

Metabolites exuded by primary producers comprise a significant fraction of marine dissolved organic matter, a poorly characterized, heterogenous mixture that dictates microbial metabolism and biogeochemical cycling. We present a foundational untargeted molecular analysis of exudates released by coral reef primary producers using liquid chromatography-tandem mass spectrometry to examine compounds produced by two coral species and three types of algae (macroalgae, turfing microalgae, and crustose coralline algae [CCA]) from Mo'orea, French Polynesia. Of 10,568 distinct ion features recovered from reef and mesocosm waters, 1,667 were exuded by producers; the majority (86%) were organism specific, reflecting a clear divide between coral and algal exometabolomes. These data allowed us to examine two tenets of coral reef ecology at the molecular level. First, stoichiometric analyses show a significantly reduced nominal carbon oxidation state of algal exometabolites than coral exometabolites, illustrating one ecological mechanism by which algal phase shifts engender fundamental changes in the biogeochemistry of reef biomes. Second, coral and algal exometabolomes were differentially enriched in organic macronutrients, revealing a mechanism for reef nutrient-recycling. Coral exometabolomes were enriched in diverse sources of nitrogen and phosphorus, including tyrosine derivatives, oleoyl-taurines, and acyl carnitines. Exometabolites of CCA and turf algae were significantly enriched in nitrogen with distinct signals from polyketide macrolactams and alkaloids, respectively. Macroalgal exometabolomes were dominated by nonnitrogenous compounds, including diverse prenol lipids and steroids. This study provides molecular-level insights into biogeochemical cycling on coral reefs and illustrates how changing benthic cover on reefs influences reef water chemistry with implications for microbial metabolism.

0s and 1s in marine molecular research: a regional HPC perspective.

High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade's experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility's future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.

Assessing the efficiency of low-cost cleaning methods for diatoms from intertidal sediment samples.

This study aims to compare the effectiveness of several low-cost reagents in obtaining high-quality diatom slides for microphytobenthos research. We evaluated the performance of eight reagents in sediment samples of beach intertidal zones. For each of the tested reagents, different pre-treatment conditions (pre-washed; non-washed) and three different temperatures (room temperature at 26 °C, 60 °C, and 100 °C) were also evaluated. For each treatment (combinations between reagents, temperatures, and pre-treatment conditions), we counted diatoms cells that met the criteria necessary for taxonomic identification (Whole/Half frustules or valves without cell material) in 30 randomly chosen fields of view in definitive preparations made from the treated samples. We also compared the treatments regarding species richness and diversity observed in the definitive preparations. The reagents influenced more the conditions of diatoms cells than the temperature and pre-treatment. H2O2, HNO3, NaClO were the methods that had the best performance in relation to the number of identifiable items. The six treatments with H2O2 presented similar amounts of identifiable items, regardless of pre-treatment and temperature. HNO3 presented a higher number of identifiable items in non-washed and pre-washed treatments at 60 °C and non-washed at 100 °C. NaClO had its best performance the following treatments: non-washed at room temperature and non-washed and pre-washed at 60 °C. H2O2 and HNO3 also showed better results for diatom species richness and diversity, followed by NaClO. The use of H2O2 was more robust since it obtained good results regardless of temperature and pre-treatments and should be preferred. HNO3 and NaClO should be used only with the appropriate temperatures, and pre-washing should be avoided.

Social survival: Humpback whales (Megaptera novaeangliae) use social structure to partition ecological niches within proposed critical habitat.

Animal culture and social bonds are relevant to wildlife conservation because they influence patterns of geography, behavior, and strategies of survival. Numerous examples of socially-driven habitat partitioning and ecological-niche specialization can be found among vertebrates, including toothed whales. But such social-ecological dynamics, described here as 'social niche partitioning', are not known among baleen whales, whose societies-particularly on foraging grounds-are largely perceived as unstructured and incidental to matters of habitat use and conservation. However, through 16 years of behavioral observations and photo-identifications of humpback whales (Megaptera novaeangliae) feeding within a fjord system in the Canadian Pacific (primarily within Gitga'at First Nation waters), we have documented long-term pair bonds (up to 12 years) as well as a complex societal structure, which corresponds closely to persistent patterns in feeding strategy, long-term site fidelity (extended occupancy and annual rate of return up to 75%), specific geographic preferences within the fjord system, and other forms of habitat use. Randomization tests of network congruency and clustering algorithms were used to test for overlap in patterns of social structure and habitat use, which confirmed the occurrence of social niche partitioning on the feeding grounds of this baleen whale species. In addition, we document the extensive practice of group bubble net feeding in Pacific Canada. This coordinated feeding behavior was found to strongly mediate the social structure and habitat use within this humpback whale society. Additionally, during our 2004-2019 study, we observed a shift in social network structure in 2010-2012, which corresponded with environmental and demographic shifts including a sudden decline in the population's calving rate. Our findings indicate that the social lives of humpback whales, and perhaps baleen whales generally, are more complex than previously supposed and should be a primary consideration in the assessment of potential impacts to important habitat.

Zinc isotopes from archaeological bones provide reliable tropic level information for marine mammals.

In marine ecology, dietary interpretations of faunal assemblages often rely on nitrogen isotopes as the main or only applicable trophic level tracer. We investigate the geographic variability and trophic level isotopic discrimination factors of bone zinc 66Zn/64Zn ratios (δ66Zn value) and compared it to collagen nitrogen and carbon stable isotope (δ15N and δ13C) values. Focusing on ringed seals (Pusa hispida) and polar bears (Ursus maritimus) from multiple Arctic archaeological sites, we investigate trophic interactions between predator and prey over a broad geographic area. All proxies show variability among sites, influenced by the regional food web baselines. However, δ66Zn shows a significantly higher homogeneity among different sites. We observe a clear trophic spacing for δ15N and δ66Zn values in all locations, yet δ66Zn analysis allows a more direct dietary comparability between spatially and temporally distinct locations than what is possible by δ15N and δ13C analysis alone. When combining all three proxies, a more detailed and refined dietary analysis is possible.

Biogeography and ecology of Ostracoda in the U.S. northern Bering, Chukchi, and Beaufort Seas.

Ostracoda (bivalved Crustacea) comprise a significant part of the benthic meiofauna in the Pacific-Arctic region, including more than 50 species, many with identifiable ecological tolerances. These species hold potential as useful indicators of past and future ecosystem changes. In this study, we examined benthic ostracodes from nearly 300 surface sediment samples, >34,000 specimens, from three regions-the northern Bering, Chukchi and Beaufort Seas-to establish species' ecology and distribution. Samples were collected during various sampling programs from 1970 through 2018 on the continental shelves at 20 to ~100m water depth. Ordination analyses using species' relative frequencies identified six species, Normanicythere leioderma, Sarsicytheridea bradii, Paracyprideis pseudopunctillata, Semicytherura complanata, Schizocythere ikeyai, and Munseyella mananensis, as having diagnostic habitat ranges in bottom water temperatures, salinities, sediment substrates and/or food sources. Species relative abundances and distributions can be used to infer past bottom environmental conditions in sediment archives for paleo-reconstructions and to characterize potential changes in Pacific-Arctic ecosystems in future sampling studies. Statistical analyses further showed ostracode assemblages grouped by the summer water masses influencing the area. Offshore-to-nearshore transects of samples across different water masses showed that complex water mass characteristics, such as bottom temperature, productivity, as well as sediment texture, influenced the relative frequencies of ostracode species over small spatial scales. On the larger biogeographic scale, synoptic ordination analyses showed dominant species-N. leioderma (Bering Sea), P. pseudopunctillata (offshore Chukchi and Beaufort Seas), and S. bradii (all regions)-remained fairly constant over recent decades. However, during 2013-2018, northern Pacific species M. mananensis and S. ikeyai increased in abundance by small but significant proportions in the Chukchi Sea region compared to earlier years. It is yet unclear if these assemblage changes signify a meiofaunal response to changing water mass properties and if this trend will continue in the future. Our new ecological data on ostracode species and biogeography suggest these hypotheses can be tested with future benthic monitoring efforts.

Effects of temperature on the behaviour and metabolism of an intertidal foraminifera and consequences for benthic ecosystem functioning.

Heatwaves have increased in intensity, duration and frequency over the last decades due to climate change. Intertidal species, living in a highly variable environment, are likely to be exposed to such heatwaves since they can be emerged for more than 6 h during a tidal cycle. Little is known, however, on how temperature affects species traits (e.g. locomotion and behaviour) of slow-moving organisms such as benthic foraminifera (single-celled protists), which abound in marine sediments. Here, we examine how temperature influences motion-behaviour and metabolic traits of the dominant temperate foraminifera Haynesina germanica by exposing individuals to usual (6, 12, 18, 24, 30 °C) and extreme (high; i.e. 32, 34, 36 °C) temperature regimes. Our results show that individuals reduced their activity by up to 80% under high temperature regimes whereas they remained active under the temperatures they usually experience in the field. When exposed to a hyper-thermic stress (i.e. 36 °C), all individuals remained burrowed and the photosynthetic activity of their sequestered chloroplasts significantly decreased. Recovery experiments subsequently revealed that individuals initially exposed to a high thermal regime partially recovered when the hyper-thermic stress ceased. H. germanica contribution to surface sediment reworking substantially diminished from 10 mm3 indiv-1 day-1 (usual temperature) to 0 mm3 indiv-1 day-1 when individuals were exposed to high temperature regimes (i.e. above 32 °C). Given their role in sediment reworking and organic matter remineralisation, our results suggest that heatwaves may have profound long-lasting effects on the functioning of intertidal muddy ecosystems and some key biogeochemical cycles.

Marine Biotechnology: Challenges and Development Market Trends for the Enhancement of Biotic Resources in Industrial Pharmaceutical and Food Applications. A Statistical Analysis of Scientific Literature and Business Models.

Biotechnology is an essential tool for the sustainable exploitation of marine resources, although the full development of their potential is complicated by a series of cognitive and technological limitations. Thanks to an innovative systematic approach that combines the meta-analysis of 620 articles produced worldwide with 29 high TRL (Technology Readiness Level) European funded projects, the study provides an assessment of the growth prospects of blue biotechnologies, with a focus on pharmaceutical and food applications, and the most promising technologies to overcome the main challenges in the commercialization of marine products. The results show a positive development trend, with publications more than doubled from 2010 (36) to 2019 (70). Biochemical and molecular characterization, with 150 studies, is the most widely used technology. However, the emerging technologies in basic research are omics technologies, pharmacological analysis and bioinformatics, which have doubled the number of publications in the last five years. On the other hand, technologies for optimizing the conditions of cultivation, harvesting and extraction are central to most business models with immediate commercial exploitation (65% of high-TRL selected projects), especially in food and nutraceutical applications. This research offers a starting point for future research to overcome all those obstacles that restrict the marketing of products derived from organisms.

Environmental stressors, complex interactions and marine benthic communities' responses.

The increasing number and diversity of anthropogenic stressors in marine habitats have multiple negative impacts on biological systems, biodiversity and ecosystem functions. Methods to assess cumulative effects include experimental manipulations, which may identify non-linear responses (i.e. synergies, antagonisms). However, experiments designed to test these ideas are uncommon, generally focusing on single biological responses. We conducted a manipulative experiment to investigate the isolated and combined effects of warming (+ 6 °C), salinity variation (freshwater pulses or presses), and nutrient enrichment (natural or enriched) following one and three month's exposure, on responses measured at multiple levels of biological complexity in a simple bivalve assemblage. More specifically, we determined effects on bivalve mortality, growth, shell mineralization, and energy content, as well as microphytobenthos biomass. Salinity variation and nutrient enrichment, individually and combined, caused strong impacts on some of the measured variables and their effect varied through time. In contrast, warming had no effect. Our work highlights the prevalence of antagonistic interactions, the importance of examining effects of single and multiple stressors through time, and of considering multiple responses to understand the complexity behind stressor interactions.

Blue whales.

Jeremy Goldbogen introduces blue whales, the largest animals to ever inhabit earth.

Reefing Viability Index for Rigs-to-Reefs (R2R) in Malaysia.

Decommissioning of the offshore platform as an artificial reef, known as Rigs-to-Reefs (R2R), has become a sustainable approach for oil companies. The platform was reused to serve the underwater ecosystem as an artificial reef for a new marine ecosystem which helps to tackle food security issue. This paper presents the findings of the formulation of the reefing viability index to recognize an offshore region that can be used for R2R projects within the South China Sea. The combined effects of spatial data, numerical modelling, and geographic system (GIS) are proposed to study the relationship of spawning ground coral reefs, diversity, and planula larvae in the process of colonization to establish a map of the reef potential environment. Coral connectivity and spawning behaviour were studied to determine the possible source of coral seedling released during the spawning season, twice a year. A geographic reef viability index was established consisting of seven parameters which are coral larval density, pelagic larval length, sea currents, temperature, chlorophyll-a, depth, and substrate availability. The ocean hydrodynamic model was designed to resemble the pattern of larval scattering. By using the simulations and rankings, there were 95 (21%) sites which could probably be used for in situ reefing, whereas 358 (79%) sites were likely ideal for ex situ reefing. Validation of the viability index was carried out using media footage assessment of remotely operated vehicle (ROV).

Larval behaviour, dispersal and population connectivity in the deep sea.

Ecosystem connectivity is an essential consideration for marine spatial planning of competing interests in the deep sea. Immobile, adult communities are connected through freely floating larvae, depending on new recruits for their health and to adapt to external pressures. We hypothesize that the vertical swimming ability of deep-sea larvae, before they permanently settle at the bottom, is one way larvae can control dispersal. We test this hypothesis with more than [Formula: see text] simulated particles with a range of active swimming behaviours embedded within the currents of a high-resolution ocean model. Despite much stronger horizontal ocean currents, vertical swimming of simulated larvae can have an order of magnitude impact on dispersal. These strong relationships between larval dispersal, pathways, and active swimming demonstrate that lack of data on larval behaviour traits is a serious impediment to modelling deep-sea ecosystem connectivity; this uncertainty greatly limits our ability to develop ecologically coherent marine protected area networks.

Rapid screening of marine bacterial symbionts using MALDI-TOF MS.

Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) is a rapid, cost-effective and high-throughput method for bacteria characterization. However, most previous studies focused on clinical isolates. In this study, we evaluated the use of MALDI-TOF MS as a rapid screening tool for marine bacterial symbionts. A set of 255 isolates from different marine sources (corals, sponge, fish and seawater) was analyzed using cell lysates to obtain a rapid grouping. Cluster analysis of mass spectra and 16S rRNA showed 18 groups, including Vibrio, Bacillus, Pseudovibrio, Alteromonas and Ruegeria. MALDI-TOF distance similarity scores ≥ 60% and ≥ 70% correspond to ≥ 98.7% 16S rRNA gene sequence similarity and ≥ 95% pyrH gene sequence similarity, respectively. MALDI-TOF MS is a useful tool for Vibrio species groups' identification.

A New Method for Collecting Large Amounts of Symbiotic Gastrodermal Cells from Octocorals.

The study of cnidarian-dinoflagellate endosymbiosis in octocorals is becoming increasingly important. As symbiotic gastrodermal cells (SGCs) are the key cells in a symbiotic relationship, obtaining SGCs and studying their functions represent an urgent need. The majority of the cells dissociated from octocoral tissues consist of host cells and algal cells, and very few intact SGCs can be observed. To solve this problem, we developed a new method to collect large amounts of SGCs from octocorals. We incubated the tissue of Sinularia flexibilis in high-salinity (60‱) filtered seawater for 6 h and were able to collect more than 18 times the number of SGCs from the control group. To test the quality of the dissociated cells, we performed three assays to evaluate their cell viability. All three assays demonstrated that cell viability was good after incubating in a high-salinity solution. We also used two other octocorals, Paralemnalia thyrsoides and Sinularia compressa, to perform the same experiment, and the results were similar to those for Sinularia flexibilis. Therefore, a high-salinity-induced increase in the SGC ratio is a common phenomenon among octocorals. This method allows researchers to collect large amounts of SGCs from octocorals and helps us to better understand the complex molecular interactions in cnidarian-dinoflagellate endosymbiosis.

An automated aquatic rack system for rearing marine invertebrates.

BACKGROUND: One hundred years ago, marine organisms were the dominant systems for the study of developmental biology. The challenges in rearing these organisms outside of a marine setting ultimately contributed to a shift towards work on a smaller number of so-called model systems. Those animals are typically non-marine organisms with advantages afforded by short life cycles, high fecundity, and relative ease in laboratory culture. However, a full understanding of biodiversity, evolution, and anthropogenic effects on biological systems requires a broader survey of development in the animal kingdom. To this day, marine organisms remain relatively understudied, particularly the members of the Lophotrochozoa (Spiralia), which include well over one third of the metazoan phyla (such as the annelids, mollusks, flatworms) and exhibit a tremendous diversity of body plans and developmental modes. To facilitate studies of this group, we have previously described the development and culture of one lophotrochozoan representative, the slipper snail Crepidula atrasolea, which is easy to rear in recirculating marine aquaria. Lab-based culture and rearing of larger populations of animals remain a general challenge for many marine organisms, particularly for inland laboratories. RESULTS: Here, we describe the development of an automated marine aquatic rack system for the high-density culture of marine species, which is particularly well suited for rearing filter-feeding animals. Based on existing freshwater recirculating aquatic rack systems, our system is specific to the needs of marine organisms and incorporates robust filtration measures to eliminate wastes, reducing the need for regular water changes. In addition, this system incorporates sensors and associated equipment for automated assessment and adjustment of water quality. An automated feeding system permits precise delivery of liquid food (e.g., phytoplankton) throughout the day, mimicking real-life feeding conditions that contribute to increased growth rates and fecundity. CONCLUSION: This automated system makes laboratory culture of marine animals feasible for both large and small research groups, significantly reducing the time, labor, and overall costs needed to rear these organisms.

The Hierarchic Treatment of Marine Ecological Information from Spatial Networks of Benthic Platforms.

Measuring biodiversity simultaneously in different locations, at different temporal scales, and over wide spatial scales is of strategic importance for the improvement of our understanding of the functioning of marine ecosystems and for the conservation of their biodiversity. Monitoring networks of cabled observatories, along with other docked autonomous systems (e.g., Remotely Operated Vehicles [ROVs], Autonomous Underwater Vehicles [AUVs], and crawlers), are being conceived and established at a spatial scale capable of tracking energy fluxes across benthic and pelagic compartments, as well as across geographic ecotones. At the same time, optoacoustic imaging is sustaining an unprecedented expansion in marine ecological monitoring, enabling the acquisition of new biological and environmental data at an appropriate spatiotemporal scale. At this stage, one of the main problems for an effective application of these technologies is the processing, storage, and treatment of the acquired complex ecological information. Here, we provide a conceptual overview on the technological developments in the multiparametric generation, storage, and automated hierarchic treatment of biological and environmental information required to capture the spatiotemporal complexity of a marine ecosystem. In doing so, we present a pipeline of ecological data acquisition and processing in different steps and prone to automation. We also give an example of population biomass, community richness and biodiversity data computation (as indicators for ecosystem functionality) with an Internet Operated Vehicle (a mobile crawler). Finally, we discuss the software requirements for that automated data processing at the level of cyber-infrastructures with sensor calibration and control, data banking, and ingestion into large data portals.

Ultra-gentle soft robotic fingers induce minimal transcriptomic response in a fragile marine animal.

Tessler et al. demonstrate that a 'soft' robot causes less stress to a jellyfish while handling compared to a traditional 'hard' robot.