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Recent Submissions

  • Submarine optical fiber communication provides an unrealized deep-sea observation network

    Guo, Yujian; Marin, Juan M.; Ashry, Islam; Trichili, Abderrahmen; Havlik, Michelle-Nicole; Ng, Tien Khee; Duarte, Carlos M.; Ooi, Boon S. (Scientific Reports, Springer Science and Business Media LLC, 2023-09-18) [Article]
    Oceans are crucial to human survival, providing natural resources and most of the global oxygen supply, and are responsible for a large portion of worldwide economic development. Although it is widely considered a silent world, the sea is filled with natural sounds generated by marine life and geological processes. Man-made underwater sounds, such as active sonars, maritime traffic, and offshore oil and mineral exploration, have significantly affected underwater soundscapes and species. In this work, we report on a joint optical fiber-based communication and sensing technology aiming to reduce noise pollution in the sea while providing connectivity simultaneously with a variety of underwater applications. The designed multifunctional fiber-based system enables two-way data transfer, monitoring marine life and ship movement near the deployed fiber at the sea bottom and sensing temperature. The deployed fiber is equally harnessed to transfer energy that the internet of underwater things (IoUTs) devices can harvest. The reported approach significantly reduces the costs and effects of monitoring marine ecosystems while ensuring data transfer and ocean monitoring applications and providing continuous power for submerged IoUT devices.
  • Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation

    Sanz-Saez, Isabel; Sanchez, Pablo; Salazar, Guillem; Sunagawa, Shinichi; de Vargas, Colomban; Bowler, Chris; Sullivan, Matthew B.; Wincker, Patrick; Karsenti, Eric; Pedrós-Alió, Carlos; Agusti, Susana; Gojobori, Takashi; Duarte, Carlos M.; Gasol, Josep M.; Sánchez, Olga; Acinas, Silvia G (ISME Communications, Springer Science and Business Media LLC, 2023-09-02) [Article]
    Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2–0.8 µm) and up to 45% in the largest particles (20–200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.
  • Bacterioplankton dark CO2 fixation in oligotrophic waters

    Alothman, Afrah; López-Sandoval, Daffne C.; Duarte, Carlos M.; Agusti, Susana (Biogeosciences, Copernicus GmbH, 2023-08-31) [Article]
    Dark CO2 fixation by bacteria is believed to be particularly important in oligotrophic ecosystems. However, only a few studies have characterized the role of bacterial dissolved inorganic carbon (DIC) fixation in global carbon dynamics. Therefore, this study quantified the primary production (PP), total bacteria dark CO2 fixation (TBDIC fixation), and heterotrophic bacterial production (HBP) in the warm and oligotrophic Red Sea using stable-isotope labeling and cavity ring-down spectroscopy (13C–CRDS). Additionally, we assessed the contribution of bacterial DIC fixation (TBDIC %) relative to the total DIC fixation (totalDIC fixation). Our study demonstrated that TBDIC fixation increased the totalDIC fixation from 2.03 to 60.45 µg C L−1 d−1 within the photic zone, contributing 13.18 % to 71.68 % with an average value of 33.95 ± 0.02 % of the photic layer totalDIC fixation. The highest TBDIC fixation values were measured at the surface and deep (400 m) water with an average value of 5.23 ± 0.45 and 4.95 ± 1.33 µg C L−1 d−1, respectively. These findings suggest that the non-photosynthetic processes such as anaplerotic DIC reactions and chemoautotrophic CO2 fixation extended to the entire oxygenated water column. On the other hand, the percent of TBDIC contribution to totalDIC fixation increased as primary production decreased (R2=0.45, p<0.0001), suggesting the relevance of increased dark DIC fixation when photosynthetic production was low or absent, as observed in other systems. Therefore, when estimating the total carbon dioxide production in the ocean, dark DIC fixation must also be accounted for as a crucial component of the carbon dioxide flux in addition to photosynthesis.
  • Gill-associated bacteria are homogeneously selected in amphibious mangrove crabs to sustain host intertidal adaptation.

    Fusi, Marco; Ngugi, David; Marasco, Ramona; Booth, Jenny Marie; Cardinale, Massimiliano; Sacchi, Luciano; Clementi, Emanuela; Yang, Xinyuan; Garuglieri, Elisa; Fodelianakis, Stylianos; Michoud, Gregoire; Daffonchio, Daniele (Microbiome, Springer Science and Business Media LLC, 2023-08-24) [Article]
    Background: The transition from water to air is a key event in the evolution of many marine organisms to access new food sources, escape water hypoxia, and exploit the higher and temperature-independent oxygen concentration of air. Despite the importance of microorganisms in host adaptation, their contribution to overcoming the challenges posed by the lifestyle changes from water to land is not well understood. To address this, we examined how microbial association with a key multifunctional organ, the gill, is involved in the intertidal adaptation of fiddler crabs, a dual-breathing organism. Results: Electron microscopy revealed a rod-shaped bacterial layer tightly connected to the gill lamellae of the five crab species sampled across a latitudinal gradient from the central Red Sea to the southern Indian Ocean. The gill bacterial community diversity assessed with 16S rRNA gene amplicon sequencing was consistently low across crab species, and the same actinobacterial group, namely Ilumatobacter, was dominant regardless of the geographic location of the host. Using metagenomics and metatranscriptomics, we detected that these members of actinobacteria are potentially able to convert ammonia to amino acids and may help eliminate toxic sulphur compounds and carbon monoxide to which crabs are constantly exposed. Conclusions: These results indicate that bacteria selected on gills can play a role in the adaptation of animals in dynamic intertidal ecosystems. Hence, this relationship is likely to be important in the ecological and evolutionary processes of the transition from water to air and deserves further attention, including the ontogenetic onset of this association. Video Abstract.
  • Influence of environmental variables on the abundance of Synapta maculata (Holothuroidea: Synaptidae) in a multi-species seagrass meadow in the southern Red Sea of Saudi Arabia

    Abrogueña, Jeff Bogart R.; Tanita, Iwao; Anton, Andrea; Maquirang, Jean Rose H.; Duarte, Carlos M.; Woo, Sau Pinn; Berković, Buga; Roje-Busatto, Romana; Yacoubi, Lamia; Doyle, Anthony; Konji, Hatem; Al-Johani, Thamer; Chen, Jia Lun; Rabaoui, Lotfi J. (Regional Studies in Marine Science, Elsevier BV, 2023-08-23) [Article]
    The Red Sea is a harsh environment characterized by high salinity and temperature, and how benthic organisms respond to the environment therein is still relatively unexplored. Here, we looked at the intertidal population of the snake sea cucumber, Synapta maculata, found in a species-rich seagrass meadow on the southern coast of the Red Sea in Saudi Arabia. The objectives of the study were (1) to examine the changes in S. maculata abundance from spring to fall in a multi-species seagrass meadow (Halodule pinifolia, Halodule univervis, Halophila ovalis, and Halophila stipulacea) and (2) to determine the relationship between the abundance of S. maculata with the selected abiotic environmental variables (depth, salinity, temperature, pH, dissolved oxygen, wind speed, wind direction, air temperature, relative humidity, and barometric pressure). The abundance of S. maculata was assessed using three permanent 50 × 4 m belt transects. Results showed that the abundance of S. maculata was present from March to June (approximately 4 individuals per 200 m2). We observed a drastic decline in the following months that coincided with the die-off of the seagrass meadow. The abundance of S. maculata differed significantly among sampling months. Correlation analysis revealed a significant positive relationship between the abundance of S. maculata and dissolved oxygen, wind speed, and barometric pressure. At the same time, salinity, water temperature, and air temperature showed a significant negative relationship. The generalized linear model suggested salinity, pH, and dissolved oxygen were the main environmental factors that influence the population of S. maculata. Overall, the population dynamics of S. maculata in this area was driven by the combination of extreme abiotic environmental factors and the presence of seagrass meadows.
  • Ideas and perspectives: The fluctuating nature of oxygen shapes the ecology of aquatic habitats and their biogeochemical cycles – the aquatic oxyscape

    Fusi, Marco; Rigaud, Sylvain; Guadagnin, Giovanna; Barausse, Alberto; Marasco, Ramona; Daffonchio, Daniele; Régis, Julie; Huchet, Louison; Camin, Capucine; Pettit, Laura; Vina-Herbon, Cristina; Giomi, Folco (Biogeosciences, Copernicus GmbH, 2023-08-23) [Article]
    Oxygen availability is a pivotal factor for ecosystem functioning and the resistance of organisms to the effect of climate change in aquatic habitats. Although extensive work has been done to assess the effect of oxygen on marine and freshwater biota, many studies have not captured the ecological importance of oxygen variations. Overlooking the fluctuating nature of oxygen may cause potential biases in the design and implementation of management policies for aquatic habitats. Conceptual perspectives on the dynamic nature of oxygen fluctuations have been raised in the scientific community in order to enhance the understanding of the effect of oxygen on the physiology and the ecology of aquatic species as well as the biogeochemical functioning of their ecosystems. A growing number of empirical work has been outlining a novel conceptual framework that considers the magnitude of oxygen fluctuation as a key variable that explains adaptation to stress conditions. Oxygen in productive aquatic habitats shows large fluctuations at the diel scale, exposing aquatic species to conditions ranging from extreme supersaturation to anoxia. Recent research has indicated that such a fluctuation tunes the physiological plasticity of the animal in response to thermal stresses. In this paper, we provide compelling evidence based on current research that the fluctuating oxygen landscape, here defined as “oxyscape”, has an important role in aquatic animal physiology and adaptation as well as the ecosystem biogeochemistry. We propose that the oxyscape should be considered in the modelling and managing policies of aquatic ecosystems.
  • Assessing the feasibility of assisted migration of corals in the Red Sea

    Barreto, Marcelle Muniz; Schmidt-Roach, Sebastian; Zhong, Huawen; Aranda, Manuel (Frontiers in Marine Science, Frontiers Media SA, 2023-08-21) [Article]
    Climate change, and in particular the unprecedented rapid global warming, presents a major threat to corals, with warming rates potentially exceeding the adaptive capacities of most coral species. Assisted gene flow, the human facilitated introduction of temperature resilience alleles from warmer to threatened colder populations via the movement of individuals (assisted migration) or their gametes (selective breeding), has been suggested as a tool to transfer thermal adaptations among populations. Due to its strong latitudinal temperature gradient and extreme temperature conditions, the Red Sea constitutes an ideal location to investigate the potential of this strategy. Here, we relocated Porites lobata colonies from three reefs along the Saudi Arabian Red Sea with different mean sea surface temperature summer maxima (ranging from 30.9 °C in Duba, 32.5 °C in Thuwal, to 33.8 °C in Jazan) to a common garden experiment in the intermediate central location. Five colonies from each location were fragmented and deployed in situ in early summer of 2018 to investigate physiological differences in bleaching, survival, and growth. Results showed significantly higher bleaching in fragments from Duba, followed by 65% mortality. Even though no bleaching was observed in fragments from Jazan, mortality rates of around 20% indicated that other environmental parameters besides temperature might influence coral health and survival. These results suggest that assisted gene flow via translocation alone may be restricted in its success due to a lack of local adaptations to environmental conditions other than temperature. However, strategies like inter-populational breeding may overcome these limitations as they might allow producing offspring with both increased thermal tolerance and local adaptations.
  • Distribution patterns of phytoplankton groups along isoirradiance layers in oligotrophic tropical and subtropical oceans

    Latasa, Mikel; Rodríguez, Francisco; Agusti, Susana; Estrada, Marta (Progress in Oceanography, Elsevier BV, 2023-08-19) [Article]
    A pigment chemotaxonomic approach was used to find the distribution of phytoplankton groups over a wide extension of the oligotrophic tropical and subtropical Atlantic, Indian and Pacific oceans. The six sampling depths corresponded to percentages of surface irradiance, i.e. “isoirradiances”. Most of the 139 stations sampled presented a subsurface deep chlorophyll maximum (DCM). Only in 19 of the 818 samples the total chlorophyll a (TChl a) concentration was >0.5 mg m−3 and only in one >0.75 mg m−3. The composition of the phytoplankton populations showed low variability. Haptophytes and Prochlorococcus contributed most to TChl a (36% and 35%, respectively), followed by green algae (11%), Synechococcus (6.5%), pelagophytes (6.7%), dinoflagellates (3.2%) and diatoms (1.6%). Specific non-polar Chl c2 pigments were analyzed to estimate the pigment biomass of three types of haptophytes (6, 7 and 8) using CHEMTAX. Haptotophytes-8 was the most abundant (18%), while haptophytes-7 and -6 contribution was 13% and 5.2%, respectively. There was a vertical partition of the groups along the water column. Prochlorococcus, haptophytes-6 and -8, and pelagophytes presented low values in shallow and intermediate layers and a strong increase in pigment biomass at the DCM. Dinoflagellates, haptophytes-7 and green algae also with low values in the upper layers showed a sharp increase at the layer above the DCM, with similar values as in the DCM or even higher for green algae. The pigment biomass of diatoms and Synechococcus were fairly homogeneous throughout the water column. These three patterns were best reflected by estimating the contribution of each group to the TChl a concentration. The Malaspina expedition crossed some well recognized ecosystem/areas of the open ocean such as the Atlantic and Pacific equatorial upwellings, the Costa Rica and Guinea domes, the low oxygen area of the northeastern Pacific and the Great Australian Bight, for which the composition of the phytoplankton populations is provided.
  • Data from: Mesophotic Foraminiferal-Algal Nodules play a role in the Red Sea carbonate budget

    Bracchi, V. A.; Purkis, Sam J.; Marchese, Fabio; Nolan, Megan K. B.; Terraneo, Tullia Isotta; Vimercati, Silvia; Chimienti, Giovanni; Rodrigue, Mattie; Eweida, Ameer; Benzoni, Francesca (Dryad, 2023-08-16) [Dataset]
    Free-living mesophotic Foraminiferal-Algal Nodules (FANs) have been discovered along the coast of the northern Saudi Arabian Red Sea (NEOM region) where they form a novel benthic ecosystem in mesophotic water depths on the continental shelf. Being mostly spheroidal, the nodules are transported en masse down slope, into the deep water of the basin, where they stop accreting. Radiometric dating informs that FANs can be more than two thousand years old and that they collectively contribute up to 66 g m-2 year-1 to the mesophotic benthic carbonate budget and account for at least 980 megatons of CaCO3, a substantial contribution considering the depauperate production of carbonate by other means in this light-limited environment. Our findings advance the knowledge of mesophotic biodiversity and carbonate production, and provide data that will inform conservation policies in the Saudi Arabian Red Sea.
  • Distribution of global sea turtle nesting explained from regional-scale coastal characteristics

    Christiaanse, Jakob C.; Antolínez, José A. A.; Luijendijk, Arjen P.; Athanasiou, Panagiotis; Duarte, Carlos M.; Aarninkhof, Stefan (Research Square Platform LLC, 2023-08-15) [Preprint]
    Climate change and human activity threaten sea turtle nesting beaches through increased flooding and erosion. Understanding the environmental characteristics that enable nesting can aid to preserve and expand these habitats. While numerous local studies exist, a comprehensive global analysis of environmental influences on the distribution of sea turtle nesting habitats remains largely unexplored. Here, we relate global sea turtle nesting distribution to 22 coastal indicators, spanning hydrodynamic, atmospheric, geophysical, habitat, and human processes. Using state-of-the-art global datasets and a novel 50-km-resolution hexagonal coastline grid (Coastgons), we employ machine learning to identify spatially homogeneous patterns in the indicators and correlate these to the occurrence of nesting grounds. Our findings suggest sea surface temperature, tidal range, extreme surges, and proximity to coral and seagrass habitats significantly influence global nesting distribution. Low tidal ranges and low extreme surges appear to be particularly favorable for individual species, likely due to reduced nest flooding. Other indicators, previously reported as influential (e.g., precipitation and wind speed), were not as important in our global-scale analysis. Finally, we identify new, potentially suitable nesting regions for each species, showing that on average 23% of global coastal regions between -37◦ and 48◦ latitude could be suitable for nesting, while only 6% is currently used by turtles. Our results help identify suitable nesting conditions, quantify potential hazards to global nesting habitats, and lay a foundation for nature-based solutions to preserve and potentially expand these habitats.
  • Carbon sequestration potential of transplanted mangroves and exotic saltmarsh plants in the sediments of subtropical wetlands.

    Huang, Runqiu; He, Junyu; Wang, Nan; Christakos, George; Gu, Jiali; Song, Li; Luo, Ji; Agusti, Susana; Duarte, Carlos M.; Wu, Jiaping (The Science of the total environment, Elsevier BV, 2023-08-15) [Article]
    Coastal blue carbon ecosystems offer promising benefits for both climate change mitigation and adaptation. While there have been widespread efforts to transplant mangroves from the tropics to the subtropics and to introduce exotic saltmarsh plants like Spartina alterniflora in China, few studies have thoroughly quantified the chronological records of carbon sequestration with different organic carbon (OC) sources. To understand how variations in OC sources can affect the carbon sequestration potential of coastal wetland environment over time, we conducted a study on typical islands with two scenarios: S. alterniflora invasion and mangrove transplantation. Our study determined chronological records of carbon sequestration and storage from five sediment profiles and traced changes in the OC sources using carbon stable isotope (δ13C) and C:N ratios in response to these scenarios. The S. alterniflora invasion resulted in an 84 ± 19 % increase in the OC burial rate compared to unvegetated mudflats, while mangrove transplantation resulted in a 167 ± 74 % increase in the OC burial rate compared to unvegetated mudflats. S. alterniflora and mangroves showed greater carbon sequestration potential in areas with high supplies of suspended particulate matter, while mangroves needed to grow to a certain scale to display obvious carbon sequestration benefits. In the mangrove saltmarsh ecotone, mature mangrove habitats exhibited resistance to the S. alterniflora invasion, while mangrove transplantation in the environment invaded by S. alterniflora had a significant effect on OC contribution. Besides, plant-derived OC can be exported to the surrounding environment due to the rapid turnover of sediments. The blue carbon chronosequence-based estimation of OC sources and burial rates provides a useful reference for establishing carbon accounting policies.
  • Mesophotic foraminiferal-algal nodules play a role in the Red Sea carbonate budget

    Bracchi, V. A.; Purkis, Sam J.; Marchese, Fabio; Nolan, Megan K. B.; Terraneo, Tullia Isotta; Vimercati, Silvia; Chimienti, Giovanni; Rodrigue, Mattie; Eweida, Ameer; Benzoni, Francesca (Communications Earth & Environment, Springer Science and Business Media LLC, 2023-08-14) [Article]
    During two scientific expeditions between 2020 and 2022, direct surveys led to the discovery of free-living mesophotic foraminiferal-algal nodules along the coast of the NEOM region (northern Saudi Arabian Red Sea) where they form an unexpected benthic ecosystem in mesophotic water depths on the continental shelf. Being mostly spheroidal, the nodules are transported en masse down slope, into the deep water of the basin, where they stop accreting. Radiometric dating informs that these nodules can be more than two thousand years old and that they collectively contribute up to 66 g m−2 year−1 to the mesophotic benthic carbonate budget and account for at least 980 megatons of calcium carbonate, a substantial contribution considering the depauperate production of carbonate by other means in this light-limited environment. Our findings advance the knowledge of mesophotic biodiversity and carbonate production, and provide data that will inform conservation policies in the Saudi Arabian Red Sea.
  • The dark side of the moon: first insights into the microbiome structure and function of one of the last glacier-fed streams in Africa

    Michoud, Gregoire; Kohler, Tyler J; Ezzat, Leila; Peter, Hannes; Nattabi, Juliet Kigongo; Nalwanga, Rosemary; Pramateftaki, Paraskevi; Styllas, Michail; Tolosano, Matteo; De Staercke, Vincent; Schön, Martina; Marasco, Ramona; Daffonchio, Daniele; Bourquin, Massimo; Busi, Susheel Bhanu; Battin, Tom J (Royal Society Open Science, The Royal Society, 2023-08-09) [Article]
    The glaciers on Africa's ‘Mountains of the Moon' (Rwenzori National Park, Uganda) are predicted to disappear within the next decades owing to climate change. Consequently, the glacier-fed streams (GFSs) that drain them will vanish, along with their resident microbial communities. Despite the relevance of microbial communities for performing ecosystem processes in equatorial GFSs, their ecology remains understudied. Here, we show that the benthic microbiome from the Mt. Stanley GFS is distinct at several levels from other GFSs. Specifically, several novel taxa were present, and usually common groups such as Chrysophytes and Polaromonas exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while greater than 80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS, and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.
  • Basin-scale variability in phytoplankton size-abundance spectra across the Atlantic Ocean

    González-García, Cristina; Agusti, Susana; Aiken, Jim; Bertrand, Arnaud; Bittencourt Farias, Gabriel; Bode, Antonio; Carré, Claire; Gonçalves-Araujo, Rafael; Harbour, Derek S.; Huete-Ortega, María; Melo, Pedro A.M.C.; Moreno-Ostos, Enrique; Rees, Andrew P.; Rodríguez, Jaime; da Silva, Sonia; Zubkov, Mikhail; Marañon, Emilio (Progress in Oceanography, Elsevier BV, 2023-08-08) [Article]
    Phytoplankton size structure, a major determinant of trophic structure and biogeochemical functioning in pelagic ecosystems, can be described by the slope of the size-abundance spectrum (SAS). Previous observational studies reporting spatio-temporal changes in phytoplankton SAS slope have focused on particular open-ocean or coastal environments. Therefore, the overall variability in phytoplankton SAS slope still has not been investigated over wide ranges of biomass and productivity including both oligotrophic open-ocean regions and productive coastal waters. Here we present a multi-cruise overview of the basin-scale variability in phytoplankton biomass and SAS slope across the Atlantic Ocean, covering coastal, shelf, and oceanic environments over the 50°N-50°S latitude range. We find the inverse relationship between cell size and abundance to be pervasive across the studied regions, even in highly productive coastal waters. In oceanic regions, consistent latitudinal patterns are observed in the relationship between nutricline depth, phytoplankton biomass and SAS slope. There is a strong degree of covariation between SAS slope at the surface and at the base of the euphotic layer, indicating that geographical changes in phytoplankton size structure override vertical variability. A basin-scale relationship exists between increasing resource supply, enhanced phytoplankton biomass, and progressively less steep SAS slopes, reflecting increasing importance of large cells in more productive waters. However, the relationship between ecosystem productivity and both SAS slope and mean community cell size is saturating, which means there is no continuous trend towards ever increasing contribution by larger cells. Similar phytoplankton size structures, with a biomass dominance by the 2–20 μm size class, are found in both moderately and highly eutrophic waters. Our results provide an observational benchmark for testing the predictions of size-based plankton models and for assessing future, climate-related shifts in phytoplankton size structure in both coastal and oceanic regions of the Atlantic Ocean.
  • Hurdles and opportunities in implementing marine biosecurity systems in data-poor regions

    Carvalho, Susana; Shchepanik, Hailey N.; Aylagas, Eva; Berumen, Michael L.; Costa, Filipe O; Costello, Mark John; Duarte, Sofia; Ferrario, Jasmine; Floerl, Oliver; Heinle, Moritz; Katsanevakis, Stelios; Marchini, Agnese; Olenin, Sergej; Pearman, John K; Peixoto, Raquel S; Rabaoui, Lotfi J; Ruiz, Greg; Srėbalienė, Greta; Therriault, Thomas W; Vieira, Pedro E; Zaiko, Anastasija (BioScience, Oxford University Press (OUP), 2023-08-07) [Article]
    Managing marine nonindigenous species (mNIS) is challenging, because marine environments are highly connected, allowing the dispersal of species across large spatial scales, including geopolitical borders. Cross-border inconsistencies in biosecurity management can promote the spread of mNIS across geopolitical borders, and incursions often go unnoticed or unreported. Collaborative surveillance programs can enhance the early detection of mNIS, when response may still be possible, and can foster capacity building around a common threat. Regional or international databases curated for mNIS can inform local monitoring programs and can foster real-time information exchange on mNIS of concern. When combined, local species reference libraries, publicly available mNIS databases, and predictive modeling can facilitate the development of biosecurity programs in regions lacking baseline data. Biosecurity programs should be practical, feasible, cost-effective, mainly focused on prevention and early detection, and be built on the collaboration and coordination of government, nongovernment organizations, stakeholders, and local citizens for a rapid response.
  • Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host.

    Villela, Helena Dias Muller; Modolon, Flúvio; Schultz, Junia; Delgadillo Ordoñez , Nathalia Catalina; Carvalho, Susana; Soriano, Adriana Ururahy; Peixoto, Raquel S (Scientific reports, Springer Science and Business Media LLC, 2023-07-28) [Article]
    Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.
  • Identification of hub genes in digestive system of mandarin fish (Siniperca chuatsi) fed with artificial diet by weighted gene co-expression network analysis.

    Shen, Yawei; Song, Lingyuan; Chen, Tiantian; Jiang, Hewei; Yang, Guokun; Zhang, Yanmin; Zhang, Xindang; Lim, Kah Kheng; Meng, Xiaolin; Zhao, Jinliang; Chen, Xiaowu (Comparative biochemistry and physiology. Part D, Genomics & proteomics, Elsevier BV, 2023-07-27) [Article]
    Mandarin fish (Siniperca chuatsi) is a carnivorous freshwater fish and an economically important species. The digestive system (liver, stomach, intestine, pyloric caecum, esophagus, and gallbladder) is an important site for studying fish domestication. In our previous study, we found that mandarin fish undergoes adaptive changes in histological morphology and gene expression levels of the digestive system when subjected to artificial diet domestication. However, we are not clear which hub genes are highly associated with domestication. In this study, we performed WGCNA on the transcriptomes of 17 tissues and 9 developmental stages and combined differentially expressed genes analysis in the digestive system to identify the hub genes that may play important functions in the adaptation of mandarin fish to bait conversion. A total of 31,657 genes in 26 samples were classified into 23 color modules via WGCNA. The modules midnightblue, darkred, lightyellow, and darkgreen highly associated with the liver, stomach, esophagus, and gallbladder were extracted, respectively. Tan module was highly related to both intestine and pyloric caecum. The hub genes in liver were cp, vtgc, c1in, c9, lect2, and klkb1. The hub genes in stomach were ghrl, atp4a, gjb3, muc5ac, duox2, and chia2. The hub genes in esophagus were mybpc1, myl2, and tpm3. The hub genes in gallbladder were dyst, npy2r, slc13a1, and slc39a4. The hub genes in the intestine and pyloric caecum were slc15a1, cdhr5, btn3a1, anpep, slc34a2, cdhr2, and ace2. Through pathway analysis, modules highly related to the digestive system were mainly enriched in digestion and absorption, metabolism, and immune-related pathways. After domestication, the hub genes vtgc and lect2 were significantly upregulated in the liver. Chia2 was significantly downregulated in the stomach. Slc15a1, anpep, and slc34a2 were significantly upregulated in the intestine. This study identified the hub genes that may play an important role in the adaptation of the digestive system to artificial diet, which provided novel evidence and ideas for further research on the domestication of mandarin fish from molecular level.
  • The roles of heating rate, intensity, and duration on the response of corals and their endosymbiotic algae to thermal stress

    Evensen, Nicolas R.; Bateman, Timothy G.; Klepac, Courtney N.; Schmidt-Roach, Sebastian; Barreto, Marcelle; Aranda, Manuel; Warner, Mark E.; Barshis, Daniel J. (Journal of Experimental Marine Biology and Ecology, Elsevier BV, 2023-07-21) [Article]
    Anthropogenic ocean warming is one of the biggest threats to marine organisms worldwide. However, it remains unclear how the duration and intensity of thermal anomalies affect organismal stress responses and thermal thresholds. We used detailed tracking of coral endosymbiont and host physiology and dose-response analyses to compare the effects of multiple heating rates, intensities, and exposure durations on two reef-building corals, Acropora hemprichii and Porites lobata, from adjacent sides of a reef (protected vs. exposed) in the Central Red Sea known to differ in high-frequency (< 24 h) temperature variability. Corals were exposed to acute heat exposures (18 h) with four target temperatures (32 °C, 35 °C, 36.5 °C, and 38 °C), versus prolonged heat exposures lasting 7–15 days where temperatures were raised 0.5 and 1.5 °C day−1 to four target temperatures (32 °C, 33.5 °C, 35 °C, and 36.5 °C). In the prolonged experiment, dose-response curves assessing algal endosymbiont Fv/Fm revealed little initial effect of temperature, before an exponential decline above 34 °C for both species. Temperature at time of measurement and degree heating hours above 34 °C (DHH34) were the variables most strongly associated with declines in Fv/Fm. The Fv/Fm thermal thresholds for P. lobata from the high-variability protected site were higher than the exposed site in the faster heating, prolonged heat stress experiment despite minimal differences in endosymbiont density, chlorophyll-a, and host protein between sites. Together, our dose-response analysis revealed complex effects of DHH34, heating rate, and species-specific differences in the influence of local thermal histories shaping thermotolerance limits for these corals.
  • Observations and biogeochemical modeling reveal chlorophyll diel cycle with near-sunset maxima in the Red Sea

    Wang, Yixin; Mazloff, Matthew R.; Verdy, Ariane; Cerovečki, I.; Naylor, Patrick; Krokos, Georgios; Hoteit, Ibrahim (Authorea, Inc., 2023-07-20) [Preprint]
    The Red Sea is an extremely warm tropical sea that hosts diverse ecosystems; thus, it is important to understand its ecology in the context of global warming. Using a coupled physical–biogeochemical model validated against in situ data, we provide the first report on the diel cycle (i.e., diel variability) in the Red Sea chlorophyll (CHL) concentration, revealing near-sunset CHL maxima at 17h ± 1h local time over the entire basin. This CHL peak time is considerably later than those reported in most other oceans, suggesting low grazing rates in this high-irradiance tropical sea. Model-based analyses reveal that CHL diel cycle is predominantly controlled by irradiance, whereas longer-timescale (e.g., seasonal) CHL variability is regulated by nutrient availability, suggesting a light-limited biological production at diel timescale. The identified CHL diel cycle comprises a fundamental component of the Red Sea ecology and has implications for CHL remote sensing and in situ measurements.
  • Editorial: Insights in aquatic microbiology: 2022.

    Zhou, Jin; Agusti, Susana (Frontiers in microbiology, Frontiers Media SA, 2023-07-19) [Article]

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