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Recent Submissions

  • Recovery of assessed global fish stocks remains uncertain

    Britten, Gregory L.; Duarte, Carlos M.; Worm, Boris (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2021-07-26) [Article]
    Concerns over overexploitation have fueled an ongoing debate on the current state and future prospects of global capture fisheries, associated threats to marine biodiversity, and declining yields available for human consumption. Management reforms have aimed to reduce fishing pressure and recover depleted stocks to biomass and exploitation rates that allow for maximum sustainable yield. Recent analyses suggest that scientifically assessed stocks, contributing over half of global marine fish catch, have, on average, reached or even exceeded these targets, suggesting a fundamental shift in the effectiveness of fisheries governance. However, such conclusions are based on calculations requiring specific choices to average over high interstock variability to derive a global trend. Here we evaluate the robustness of these conclusions by examining the distribution of recovery rates across individual stocks and by applying a diversity of plausible averaging techniques. We show that different methods produce markedly divergent trajectories of global fisheries status, with 4 of 10 methods suggesting that recovery has not yet been achieved, with up to 48% of individual stocks remaining below biomass targets and 40% exploited above sustainable rates. Furthermore, recent rates of recovery are only marginally different from zero, with up to 46% of individual stocks trending downward in biomass and 29% of stocks trending upward in exploitation rate. These results caution against overoptimistic assessments of fisheries writ large and support a precautionary management approach to ensure full rebuilding of depleted fisheries worldwide.
  • Effects of Ecological Restoration Using Non-Native Mangrove Kandelia obovata to Replace Invasive Spartina alterniflora on Intertidal Macrobenthos Community in Maoyan Island (Zhejiang, China)

    Wang, Qiuxuan; Duarte, Carlos M.; Song, Li; Christakos, George; Agusti, Susana; Wu, Jiaping (Journal of Marine Science and Engineering, MDPI AG, 2021-07-22) [Article]
    Spartina alterniflora has extensively invaded the coastline of China, including in Maoyan Island of Zhejiang Province. Ecological restoration has been conducted using non-native mangrove Kandelia obovata to replace S. alterniflora in an attempt to restore the impacted intertidal zones. To illustrate the ecological effectiveness of the restoration projects, macrobenthos communities were studied among different habitats within the restored areas, including one non-restored S. alterniflora marsh (SA) and three differently-aged restored K. obovata stands planted in 2003, 2009, and 2011 respectively (KF14, KF8, and KF6). Besides, one unvegetated mudflat (MF) adjacent to the non-restored S. alterniflora marsh and one K. obovata forest transplanted in 2006 (RKF) at a previously barren mudflat without invasion history of S. alterniflora were set as reference sites. A total of 69 species of macrobenthos were collected from Maoyan Island, and the species richness was dominated by gastropoda (23 species), polychaeta (18 species), and malacostraca (16 species). There was no significant difference between the six sites in terms of the abundance of macrobenthos, with the average values of abundance peaking in KF6 (734.7 ind m−2) and being lowest in RKF (341.3 ind m−2). The six sites had significant differences in terms of the biomass of macrobenthos. The KF8 site contained the highest average biomass (168.3 g m−2), whereas the MF site had the lowest (54.3 g m−2). The Shannon-Wiener diversity index and Pielou’s evenness index of the macrobenthos did not exhibit significant differences among the six sites. However, the results of permutational multivariate analysis of variance (PERMANOVA) revealed significant spatial differences in the macrobenthos community structure between the sites. Since KF14 shared a similar macrobenthos community structure with RKF, while representing a strikingly different structure from SA, we infer that ecological restoration using K. obovata can restore the macrobenthos community to resemble to a normally planted K. obovata forest about 15 years after restoration.
  • Seasonal M2 Internal Tides in the Arabian Sea

    Ma, Jingyi; Guo, Daquan; Zhan, Peng; Hoteit, Ibrahim (Remote Sensing, MDPI AG, 2021-07-18) [Article]
    Internal tides play a crucial role in ocean mixing. To explore the seasonal features of mode-1 M2 internal tides in the Arabian Sea, we analyzed their propagation and energy distribution using along-track sea-level anomaly data collected by satellite altimeters. We identified four primary source regions of internal tides: Abd al Kuri Island, the Carlsberg Ridge, the northeastern Arabian Sea, and the Maldive Islands. The baroclinic signals that originate from Abd al Kuri Island propagate meridionally, whereas those originating from the west coast of India propagate southwestward. The strength and energy flux of the internal tides in the Arabian Sea exhibit significant seasonal and spatial variability. The internal tides generated during winter are more energetic and can propagate further than those generated in summer. Doppler shifting and horizontal variations in stratification can explain the differences in the internal tides’ seasonal distributions.
  • Diversity, host specificity and biogeography in the Cladocorynidae (Hydrozoa, Capitata), with description of a new genus

    Maggioni, Davide; Garese, Agustín; Huang, Danwei; Hoeksema, Bert W.; Arrigoni, Roberto; Seveso, Davide; Galli, Paolo; Berumen, Michael L.; Montalbetti, Enrico; Pica, Daniela; Torsani, Fabrizio; Montano, Simone (Cladistics, Wiley, 2021-07-14) [Article]
    The hydrozoan family Cladocorynidae inhabits tropical to temperate waters and comprises the two genera Pteroclava and Cladocoryne. Pteroclava lives in association with some octocorals and hydrozoans, whereas Cladocoryne is more generalist in terms of substrate choice. This work provides a thorough morpho-molecular reassessment of the Cladocorynidae by presenting the first well-supported phylogeny of the family based on the analyses of three mitochondrial and four nuclear markers. Notably, the two nominal genera were confirmed to be monophyletic and both morphological and genetic data led to the formal description of a new genus exclusively associated with octocorals, Pseudozanclea gen. nov. Maggioni & Montano. Accordingly, the diagnosis of the family was updated. The ancestral state reconstruction of selected characters revealed that the symbiosis with octocorals likely appeared in the most recent common ancestor of Pteroclava and Pseudozanclea. Additionally, the presence of euryteles aggregation in the polyp stage and the exumbrellar nematocyst pouches with euryteles represent synapomorphies of all cladocorynid taxa and probably emerged in their most recent common ancestor. The analysis of several Pteroclava krempfi colonies from Indo-Pacific and Caribbean localities associated with several host octocorals revealed a high intra-specific genetic variability. Single- and multi-locus species delimitations resulted in three to five species hypotheses, but the statistical analysis of morphometric data showed only limited distinction among the clades of P. krempfi. However, P. krempfi clades showed differences in both host specificity, mostly at the octocoral family level, and geographic distribution, with one clade found exclusively in the Caribbean Sea and the others found in the Indo-Pacific.
  • Disentangling marine microbial networks across space

    Deutschmann, Ina Maria; Delage, Erwan; Giner, Caterina R; Sebastián, Marta; Poulain, Julie; Aristegui, Javier; Duarte, Carlos M.; Acinas, Silvia G; Massana, Ramon; Gasol, Josep M.; Eveillard, Damien; Chaffron, Samuel; Logares, Ramiro (Cold Spring Harbor Laboratory, 2021-07-13) [Preprint]
    Although microbial interactions underpin ocean ecosystem functions, they remain barely known. Different studies have analyzed microbial interactions using static association networks based on omics-data. However, microbial associations are dynamic and can change across physicochemical gradients and spatial scales, which needs to be considered to understand the ocean ecosystem better. We explored associations between archaea, bacteria, and picoeukaryotes along the water column from the surface to the deep ocean across the northern subtropical to the southern temperate ocean and the Mediterranean Sea by defining sample-specific subnetworks. Quantifying spatial association recurrence, we found the lowest fraction of global associations in the bathypelagic zone, while associations endemic of certain regions increased with depth. Overall, our results highlight the need to study the dynamic nature of plankton networks and our approach represents a step forward towards a better comprehension of the biogeography of microbial interactions across ocean regions and depth layers.
  • Year-round high abundances of the world’s smallest marine vertebrate (Schindleria) in the Red Sea and worldwide associations with lunar phases

    Robitzch Sierra, Vanessa S. N.; Molina-Valdivia, Victor; Solano-Iguaran, Jaiber J.; Landaeta, Mauricio F.; Berumen, Michael L. (Scientific Reports, Springer Science and Business Media LLC, 2021-07-12) [Article]
    AbstractVery little is known about the ecology and biology of the smallest marine vertebrates, fishes in the genus Schindleria. Even though over half of named Schindleria species have been identified in the Red Sea, the collection of only very few specimens has been documented. Here, we assessed abundance patterns of nearly two thousand Red Sea long dorsal fin (LDF) adults and found evidence for putative seasonal and spatial differences, likely related to differing habitat and environmental conditions. The highest abundances were outside local seasonal temperature extremes and decoupled from peaks of coral reef fish recruitment. We also found evidence for global trends in abundances related to lunar cycles using our Red Sea data and that from a recently published large collection of specimens from the DANA Expedition (1928–1930). The abundance of adult LDF Schindleria in relation to lunar phases differed significantly, with most Schindleria caught outside the full moon, and mostly during the new moon in the Red Sea and the 3rd quarter moon in the DANA collection. We further suggest that the abundances of Schindleria at coral reefs may be related to reproductive cycles and that these cycles may be timed with the moon as back-calculations of hatch dates from otoliths from the Red Sea significantly resulted after the new moon, making Schindleria the fastest-lived coral reef fish with the shortest generation times. Schindleria could be the most numerous coral reef fish in the world, for which we encourage increased research.
  • A comparative baseline of coral disease in three regions along the Saudi Arabian coast of the central Red Sea.

    Aeby, Greta Smith; Shore, Amanda; Jensen, Thor; Ziegler, Maren; Work, Thierry; Voolstra, Christian R. (PloS one, Public Library of Science (PLoS), 2021-07-09) [Article]
    Coral disease is a growing problem for coral reefs globally and diseases have been linked to thermal stress, excess nutrients, overfishing and other human impacts. The Red Sea is a unique environment for corals with a strong environmental gradient characterized by temperature extremes and high salinities, but minimal terrestrial runoff or riverine input and their associated pollution. Yet, relatively little is known about coral diseases in this region. Disease surveys were conducted at 22 reefs within three regions (Yanbu, Thuwal, Al Lith) in the central Red Sea along the Saudi Arabian coast. Surveys occurred in October 2015, which coincided with a hyperthermal-induced bleaching event. Our objectives were to 1) document types, prevalence, and distribution of coral diseases in a region with minimal terrestrial input, 2) compare regional differences in diseases and bleaching along a latitudinal gradient of environmental conditions, and 3) use histopathology to characterize disease lesions at the cellular level. Coral reefs of the central Red Sea had a widespread but a surprisingly low prevalence of disease (75,750 colonies. Twenty diseases were recorded affecting 16 coral taxa and included black band disease, white syndromes, endolithic hypermycosis, skeletal eroding band, growth anomalies and focal bleached patches. The three most common diseases were Acropora white syndrome (59.1% of the survey sites), Porites growth anomalies (40.9%), and Porites white syndrome (31.8%). Sixteen out of 30 coral genera within transects had lesions and Acropora, Millepora and Lobophyllia were the most commonly affected. Cell-associated microbial aggregates were found in four coral genera including a first report in Stylophora. Differences in disease prevalence, coral cover, amount of heat stress as measured by degree heating weeks (DHW) and extent of bleaching was evident among sites. Disease prevalence was not explained by coral cover or DHW, and a negative relationship between coral bleaching and disease prevalence was found. The northern-most sites off the coast of Yanbu had the highest average disease prevalence and highest average DHW values but no bleaching. Our study provides a foundation and baseline data for coral disease prevalence in the central Red Sea, which is projected to increase as a consequence of increased frequency and severity of ocean warming.
  • Reply to: Caution over the use of ecological big data for conservation.

    Queiroz, Nuno; Humphries, Nicolas E; Couto, Ana; Vedor, Marisa; da Costa, Ivo; Sequeira, Ana M M; Mucientes, Gonzalo; Santos, António M; Abascal, Francisco J; Abercrombie, Debra L; Abrantes, Katya; Acuña-Marrero, David; Afonso, André S; Afonso, Pedro; Anders, Darrell; Araujo, Gonzalo; Arauz, Randall; Bach, Pascal; Barnett, Adam; Bernal, Diego; Berumen, Michael L.; Lion, Sandra Bessudo; Bezerra, Natalia P A; Blaison, Antonin V; Block, Barbara A; Bond, Mark E; Bonfil, Ramon; Braun, Camrin D; Brooks, Edward J; Brooks, Annabelle; Brown, Judith; Byrne, Michael E; Campana, Steven E; Carlisle, Aaron B; Chapman, Demian D; Chapple, Taylor K; Chisholm, John; Clarke, Christopher R; Clua, Eric G; Cochran, Jesse E M; Crochelet, Estelle C; Dagorn, Laurent; Daly, Ryan; Cortés, Daniel Devia; Doyle, Thomas K; Drew, Michael; Duffy, Clinton A J; Erikson, Thor; Espinoza, Eduardo; Ferreira, Luciana C; Ferretti, Francesco; Filmalter, John D; Fischer, G Chris; Fitzpatrick, Richard; Fontes, Jorge; Forget, Fabien; Fowler, Mark; Francis, Malcolm P; Gallagher, Austin J; Gennari, Enrico; Goldsworthy, Simon D; Gollock, Matthew J; Green, Jonathan R; Gustafson, Johan A; Guttridge, Tristan L; Guzman, Hector M; Hammerschlag, Neil; Harman, Luke; Hazin, Fábio H V; Heard, Matthew; Hearn, Alex R; Holdsworth, John C; Holmes, Bonnie J; Howey, Lucy A; Hoyos, Mauricio; Hueter, Robert E; Hussey, Nigel E; Huveneers, Charlie; Irion, Dylan T; Jacoby, David M P; Jewell, Oliver J D; Johnson, Ryan; Jordan, Lance K B; Joyce, Warren; Keating Daly, Clare A; Ketchum, James T; Klimley, A Peter; Kock, Alison A; Koen, Pieter; Ladino, Felipe; Lana, Fernanda O; Lea, James S E; Llewellyn, Fiona; Lyon, Warrick S; MacDonnell, Anna; Macena, Bruno C L; Marshall, Heather; McAllister, Jaime D; Meÿer, Michael A; Morris, John J; Nelson, Emily R; Papastamatiou, Yannis P; Peñaherrera-Palma, Cesar; Pierce, Simon J; Poisson, Francois; Quintero, Lina Maria; Richardson, Andrew J; Rogers, Paul J; Rohner, Christoph A; Rowat, David R L; Samoilys, Melita; Semmens, Jayson M; Sheaves, Marcus; Shillinger, George; Shivji, Mahmood; Singh, Sarika; Skomal, Gregory B; Smale, Malcolm J; Snyders, Laurenne B; Soler, German; Soria, Marc; Stehfest, Kilian M; Thorrold, Simon R; Tolotti, Mariana T; Towner, Alison; Travassos, Paulo; Tyminski, John P; Vandeperre, Frederic; Vaudo, Jeremy J; Watanabe, Yuuki Y; Weber, Sam B; Wetherbee, Bradley M; White, Timothy D; Williams, Sean; Zárate, Patricia M; Harcourt, Robert; Hays, Graeme C; Meekan, Mark G; Thums, Michele; Irigoien, Xabier; Eguiluz, Victor M; Duarte, Carlos M.; Sousa, Lara L; Simpson, Samantha J; Southall, Emily J; Sims, David W (Springer Science and Business Media LLC, 2021-07-08) [Article]
  • Reply to: Shark mortality cannot be assessed by fishery overlap alone.

    Queiroz, Nuno; Humphries, Nicolas E; Couto, Ana; Vedor, Marisa; da Costa, Ivo; Sequeira, Ana M M; Mucientes, Gonzalo; Santos, António M; Abascal, Francisco J; Abercrombie, Debra L; Abrantes, Katya; Acuña-Marrero, David; Afonso, André S; Afonso, Pedro; Anders, Darrell; Araujo, Gonzalo; Arauz, Randall; Bach, Pascal; Barnett, Adam; Bernal, Diego; Berumen, Michael L.; Lion, Sandra Bessudo; Bezerra, Natalia P A; Blaison, Antonin V; Block, Barbara A; Bond, Mark E; Bonfil, Ramon; Bradford, Russell W; Braun, Camrin D; Brooks, Edward J; Brooks, Annabelle; Brown, Judith; Bruce, Barry D; Byrne, Michael E; Campana, Steven E; Carlisle, Aaron B; Chapman, Demian D; Chapple, Taylor K; Chisholm, John; Clarke, Christopher R; Clua, Eric G; Cochran, Jesse E M; Crochelet, Estelle C; Dagorn, Laurent; Daly, Ryan; Cortés, Daniel Devia; Doyle, Thomas K; Drew, Michael; Duffy, Clinton A J; Erikson, Thor; Espinoza, Eduardo; Ferreira, Luciana C; Ferretti, Francesco; Filmalter, John D; Fischer, G Chris; Fitzpatrick, Richard; Fontes, Jorge; Forget, Fabien; Fowler, Mark; Francis, Malcolm P; Gallagher, Austin J; Gennari, Enrico; Goldsworthy, Simon D; Gollock, Matthew J; Green, Jonathan R; Gustafson, Johan A; Guttridge, Tristan L; Guzman, Hector M; Hammerschlag, Neil; Harman, Luke; Hazin, Fábio H V; Heard, Matthew; Hearn, Alex R; Holdsworth, John C; Holmes, Bonnie J; Howey, Lucy A; Hoyos, Mauricio; Hueter, Robert E; Hussey, Nigel E; Huveneers, Charlie; Irion, Dylan T; Jacoby, David M P; Jewell, Oliver J D; Johnson, Ryan; Jordan, Lance K B; Joyce, Warren; Keating Daly, Clare A; Ketchum, James T; Klimley, A Peter; Kock, Alison A; Koen, Pieter; Ladino, Felipe; Lana, Fernanda O; Lea, James S E; Llewellyn, Fiona; Lyon, Warrick S; MacDonnell, Anna; Macena, Bruno C L; Marshall, Heather; McAllister, Jaime D; Meÿer, Michael A; Morris, John J; Nelson, Emily R; Papastamatiou, Yannis P; Peñaherrera-Palma, Cesar; Pierce, Simon J; Poisson, Francois; Quintero, Lina Maria; Richardson, Andrew J; Rogers, Paul J; Rohner, Christoph A; Rowat, David R L; Samoilys, Melita; Semmens, Jayson M; Sheaves, Marcus; Shillinger, George; Shivji, Mahmood; Singh, Sarika; Skomal, Gregory B; Smale, Malcolm J; Snyders, Laurenne B; Soler, German; Soria, Marc; Stehfest, Kilian M; Thorrold, Simon R; Tolotti, Mariana T; Towner, Alison; Travassos, Paulo; Tyminski, John P; Vandeperre, Frederic; Vaudo, Jeremy J; Watanabe, Yuuki Y; Weber, Sam B; Wetherbee, Bradley M; White, Timothy D; Williams, Sean; Zárate, Patricia M; Harcourt, Robert; Hays, Graeme C; Meekan, Mark G; Thums, Michele; Irigoien, Xabier; Eguiluz, Victor M; Duarte, Carlos M.; Sousa, Lara L; Simpson, Samantha J; Southall, Emily J; Sims, David W (Springer Science and Business Media LLC, 2021-07-08) [Article]
  • Mangrovivirga cuniculi gen. nov., sp. nov., a moderately halophilic bacterium isolated from bioturbated Red Sea mangrove sediment, and proposal of the novel family Mangrovivirgaceae fam. nov

    Sefrji, Fatmah; Michoud, Gregoire; Marasco, Ramona; Merlino, Giuseppe; Daffonchio, Daniele (International journal of systematic and evolutionary microbiology, Microbiology Society, 2021-07-02) [Article]
    A strictly aerobic, Gram-stain-negative, non-motile, rod-shaped bacterium, designated strain R1DC9T, was isolated from sediments of a mangrove stand on the Red Sea coast of Saudi Arabia via diffusion chamber cultivation. Strain R1DC9T grew at 20–40 °C (optimum, 37 °C), pH 6–10 (optimum, pH 8) and 3–11 % NaCl (optimum, 7–9 %) in the cultivation medium. The genome of R1DC9T was 4 661 901 bp long and featured a G+C content of 63.1 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis using 120 concatenated single-copy genes revealed that R1DC9T represents a distinct lineage in the order Cytophagales and the phylum Bacteroidetes separated from the Roseivirgaceae and Marivirgaceae families. R1DC9T displayed 90 and 89 % 16S rRNA gene sequence identities with Marivirga sericea DSM 4125T and Roseivirga ehrenbergii KMM 6017T, respectively. The predominant quinone was MK7. The polar lipids were phosphatidylethanolamine, two unknown phospholipids and two unknown lipids. The predominant cellular fatty acids were the saturated branch chain fatty acids iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 0, along with a low percentage of the monounsaturated fatty acid C16 : 1 ω5c. Based on differences in phenotypic, physiological and biochemical characteristics from known relatives, and the results of phylogenetic analyses, R1DC9T (=KCTC 72349T=JCM 33609T=NCCB 100698T) is proposed to represent a novel species in a new genus, and the name Mangrovivirga cuniculi gen. nov., sp. nov. is proposed. The distinct phylogenetic lineage among the families in the order Cytophagales indicates that R1DC9T represents a new family for which the name Mangrovivirgaceae fam. nov. is proposed.
  • Dead-reckoning animal movements in R: a reappraisal using Gundog.Tracks

    Gunner, Richard; Holton, Mark D.; Scantlebury, Mike D.; van Schalkwyk, O. Louis; English, Holly M.; Williams, Hannah J.; Hopkins, Phil; Quintana, Flavio; Gómez-Laich, Agustina; Börger, Luca; Redcliffe, James; Yoda, Ken; Yamamoto, Takashi; Ferreira, Sam; Govender, Danny; Viljoen, Pauli; Bruns, Angela; Bell, Stephen H.; Marks, Nikki J.; Bennett, Nigel C.; Tonini, Mariano H.; Duarte, Carlos M.; van Rooyen, Martin C.; Bertelsen, Mads F.; Tambling, Craig J.; Wilson, Rory P. (Animal Biotelemetry, Springer Science and Business Media LLC, 2021-07-01) [Article]
    Abstract Background Fine-scale data on animal position are increasingly enabling us to understand the details of animal movement ecology and dead-reckoning, a technique integrating motion sensor-derived information on heading and speed, can be used to reconstruct fine-scale movement paths at sub-second resolution, irrespective of the environment. On its own however, the dead-reckoning process is prone to cumulative errors, so that position estimates quickly become uncoupled from true location. Periodic ground-truthing with aligned location data (e.g., from global positioning technology) can correct for this drift between Verified Positions (VPs). We present step-by-step instructions for implementing Verified Position Correction (VPC) dead-reckoning in R using the tilt-compensated compass method, accompanied by the mathematical protocols underlying the code and improvements and extensions of this technique to reduce the trade-off between VPC rate and dead-reckoning accuracy. These protocols are all built into a user-friendly, fully annotated VPC dead-reckoning R function; Gundog.Tracks, with multi-functionality to reconstruct animal movement paths across terrestrial, aquatic, and aerial systems, provided within the Additional file 4 as well as online (GitHub). Results The Gundog.Tracks function is demonstrated on three contrasting model species (the African lion Panthera leo, the Magellanic penguin Spheniscus magellanicus, and the Imperial cormorant Leucocarbo atriceps) moving on land, in water and in air. We show the effect of uncorrected errors in speed estimations, heading inaccuracies and infrequent VPC rate and demonstrate how these issues can be addressed. Conclusions The function provided will allow anyone familiar with R to dead-reckon animal tracks readily and accurately, as the key complex issues are dealt with by Gundog.Tracks. This will help the community to consider and implement a valuable, but often overlooked method of reconstructing high-resolution animal movement paths across diverse species and systems without requiring a bespoke application.
  • Airborne Eukaryotes in the Red Sea Region

    Aalismail, Nojood; Diaz Rua, Ruben; Geraldi, Nathan; Cusack, Michael; Duarte, Carlos M. (NCBI, 2021-06-29) [Bioproject, Dataset]
    Airborne Eukaryotic Communities (AEC), rank among the least studied aerobiological components. We describe here the AECs in the global dust belt, the area between the west coast of North Africa and Central Asia, which supports the highest dust fluxes on the planet. Specifically, we sampled atmospheric dust over 14 months from onshore and offshore locations of the Red Sea, the only waterbody that entirely encompassed in the global dust belt. We also sampled surface water samples to determine the potential transfer of taxa across the air-sea interface. To target the eukaryotes, we performed Miseq sequencing of atmospheric dust and surface water samples. Analysis of amplicon sequencing indicates a total pool of 18,816 sequence variants (SVs). Among 33 unique eukaryotic phyla in the AEC over the Red Sea, the most dominant taxa were Streptophyta, Apicomplexa, and Ascomycota. Aerosol eukaryotes originated from various sources and formed more diverse communities than eukaryotic communities of the Red Sea surface water. AECs were dominated by phylotypes released from plant material and soils, and including taxa reported to be harmful to human health. The community composition was significantly influenced by sampling locations and seasonal conditions but not by the origin of the air masses nor dust loads.
  • Detection of SARS-CoV-2 variants requires urgent global coordination

    Duarte, Carlos M.; Jamil, Tahira; Gojobori, Takashi; Alam, Intikhab (International Journal of Infectious Diseases, Elsevier BV, 2021-06-17) [Article]
    Objectives We assessed the effort deployed by different nations and territories to sequence SARS-CoV-2 isolates, thus allowing the detection of variants, known and novel, of concern. Design We analyzed the sources of over one million full genome sequences of SARS-CoV-2 virus available in the COVID-19 virus Mutation Tracker (CovMT) to determine the number of variants in the RBD region of the genome determining infectivity detected in the various nations and territories. Results The number of variants detected increased as the square root of sequencing effort of sequencing effort by nations. Eight nations contributed 79% of all SARS-CoV-2 isolates sequenced, with 2/3’s of all unique variants, adding to 1118 RBD variants, reported by 5 nations. The median number of isolates sequenced required to detect, on average, one novel RBD variant is 24.05, a threshold only achieved by 70 nations. Conclusions Many developing nations have not contributed any sequences due to lack of capacity, with a risk of dangerous virus variants in these undersampled regions spreading globally before being detected. A collaborative program to sequence SARS-CoV-2 isolates, and other pathogens of concern, is needed to monitor, track and control the pandemic.
  • Analysis of the temporal and spatial variability of whale shark (Rhincodon typus) aggregation in the South Ari Marine Protected Area, Maldives, Indian Ocean

    Valsecchi, S.; Lanfredi, C.; Azzellino, A.; Savini, A.; Bracchi, V. A.; Marchese, Fabio; Hancock, J.; Rees, R.; Cánovas Pérez, C. (The European Zoological Journal, Informa UK Limited, 2021-06-17) [Article]
    Whale sharks are known to aggregate in coastal areas. In the South Ari Marine Protected Area (Maldives) a aggregation, mostly represented by young males with a high level of residency, has been described in the literature. Despite the worldwide interest in the natural resources of the Maldives, this population is increasingly subjected to anthropogenic pressure and major concern regards the flourishing tourist industry. In this study, data collected by the Maldives Whale Shark Research Programme between 2014 and 2017 have been used to detect both temporal and spatial patterns of occurrence. Favourable environmental conditions to visually detect whale sharks have been defined for the studied area. Accordingly, a total of 1077 shark encounters have been analysed in this study. Environmental conditions (i.e. sea surface temperature, monsoon occurrence) have been used to detect possible factors affecting the spatial and temporal variability of Rhincodon typus aggregations. A two-way ANOVA has been performed to detect temporal trends in animal occurrence, sea surface temperature pattern and to investigate the sea bottom depth variability during encounters. Significant differences in the monthly occurrence of whale sharks within the same year and among different years have been detected. Similar patterns have been observed for environmental parameters such as sea surface temperature and depth. A different spatial distribution has also been detected as a function of the Indian Monsoon reversal (north-eastern and south-western) affecting the area. During the northeast monsoon period, whale sharks appeared to concentrate in a smaller longitudinal range closer to the western-central part of the MPA, where deeper water conditions occur due to the proximity of a deep depression (submarine canyon). Results from this study provide new pieces of information for the implementation of dedicated management actions to protect the whale sharks population inhabiting the South Ari Marine Protected Area.
  • Uncertainty Quantification and Bayesian Inference of Cloud Parameterization in the NCAR Single Column Community Atmosphere Model (SCAM6)

    Pathak, Raju; Dasari, Hari Prasad; El Mohtar, Samah; Subramanian, Aneesh; Sahany, Sandeep; Mishra, Saroj K; Knio, Omar; Hoteit, Ibrahim (Frontiers in Climate, Frontiers, 2021-06-16) [Article]
    Uncertainty quantification (UQ) in weather and climate models is required to assess the sensitivity of their outputs to various parameterization schemes and thereby improve their consistency with observations. Herein, we present an efficient UQ and Bayesian inference for the cloud parameters of the NCAR Single Column Atmosphere Model (SCAM6) using surrogate models based on a polynomial chaos expansion. The use of a surrogate model enables to efficiently propagate uncertainties in parameters into uncertainties in model outputs. We investigated eight uncertain parameters: the auto-conversion size threshold for ice to snow (dcs), the fall speed parameter for stratiform cloud ice (ai), the fall speed parameter for stratiform snow (as), the fall speed parameter for cloud water (ac), the collection efficiency of aggregation ice (eii), the efficiency factor of the Bergeron effect (berg_eff), the threshold maximum relative humidity for ice clouds (rhmaxi), and the threshold minimum relative humidity for ice clouds (rhmini). We built two surrogate models using two non-intrusive methods: spectral projection (SP) and basis pursuit denoising (BPDN). Our results suggest that BPDN performs better than SP as it enables to filter out internal noise during the process of fitting the surrogate model. Five out of the eight parameters (namely dcs, ai, rhmaxi, rhmini, and eii) account for most of the variance in predicted climate variables (e.g., total precipitation, cloud distribution, shortwave and longwave cloud forcing, ice and liquid water path). A first-order sensitivity analysis reveals that dcs contributes approximately 40–80% of the total variance of the climate variables, ai around 15–30%, and rhmaxi, rhmini, and eii around 5–15%. The second- and higher-order effects contribute approximately 20% and 11%, respectively. The sensitivity of the model to these parameters was further explored using response curves. A Markov chain Monte Carlo (MCMC) sampling algorithm was also implemented for the Bayesian inference of dcs, ai, as, rhmini, and berg_eff using cloud distribution data collected at the Southern Great Plains (USA). Our study has implications for enhancing our understanding of the physical mechanisms associated with cloud processes leading to uncertainty in model simulations and further helps to improve the models used for their assessment.
  • Latitudinal variation in monthly-scale reproductive synchrony among Acropora coral assemblages in the Indo-Pacific

    Bouwmeester, Jessica; Edwards, Alasdair J.; Guest, James R.; Bauman, Andrew G.; Berumen, Michael L.; Baird, Andrew H. (Coral Reefs, Springer Science and Business Media LLC, 2021-06-15) [Article]
    Early research into coral reproductive biology suggested that spawning synchrony was driven by variations in the amplitude of environmental variables that are correlated with latitude, with synchrony predicted to break down at lower latitudes. More recent research has revealed that synchronous spawning, both within and among species, is a feature of all speciose coral assemblages, including equatorial reefs. Nonetheless, considerable variation in reproductive synchrony exists among locations and the hypothesis that the extent of spawning synchrony is correlated with latitude has not been formally tested on a large scale. Here, we use data from 90 sites throughout the Indo-Pacific and a quantitative index of reproductive synchrony applied at a monthly scale to demonstrate that, despite considerable spatial and temporal variation, there is no correlation between latitude and reproductive synchrony. Considering the critical role that successful reproduction plays in the persistence and recovery of coral reefs, research is urgently needed to understand the drivers underpinning variation in reproductive synchrony
  • Latitudinal variation in monthly-scale reproductive synchrony among Acropora coral assemblages in the Indo-Pacific

    Bouwmeester, Jessica; Edwards, Alasdair J.; Guest, James R.; Bauman, Andrew G.; Berumen, Michael L.; Baird, Andrew H. (Coral Reefs, Springer Science and Business Media LLC, 2021-06-15) [Article]
    Early research into coral reproductive biology suggested that spawning synchrony was driven by variations in the amplitude of environmental variables that are correlated with latitude, with synchrony predicted to break down at lower latitudes. More recent research has revealed that synchronous spawning, both within and among species, is a feature of all speciose coral assemblages, including equatorial reefs. Nonetheless, considerable variation in reproductive synchrony exists among locations and the hypothesis that the extent of spawning synchrony is correlated with latitude has not been formally tested on a large scale. Here, we use data from 90 sites throughout the Indo-Pacific and a quantitative index of reproductive synchrony applied at a monthly scale to demonstrate that, despite considerable spatial and temporal variation, there is no correlation between latitude and reproductive synchrony. Considering the critical role that successful reproduction plays in the persistence and recovery of coral reefs, research is urgently needed to understand the drivers underpinning variation in reproductive synchrony
  • An integrative investigation of sensory organ development and orientation behavior throughout the larval phase of a coral reef fish.

    Majoris, John E.; Foretich, Matthew A; Hu, Yinan; Nickles, Katie R; Di Persia, Camilla L; Chaput, Romain; Schlatter, E; Webb, Jacqueline F; Paris, Claire B; Buston, Peter M (Scientific reports, Springer Science and Business Media LLC, 2021-06-12) [Article]
    The dispersal of marine larvae determines the level of connectivity among populations, influences population dynamics, and affects evolutionary processes. Patterns of dispersal are influenced by both ocean currents and larval behavior, yet the role of behavior remains poorly understood. Here we report the first integrated study of the ontogeny of multiple sensory systems and orientation behavior throughout the larval phase of a coral reef fish-the neon goby, Elacatinus lori. We document the developmental morphology of all major sensory organs (lateral line, visual, auditory, olfactory, gustatory) together with the development of larval swimming and orientation behaviors observed in a circular arena set adrift at sea. We show that all sensory organs are present at hatch and increase in size (or number) and complexity throughout the larval phase. Further, we demonstrate that most larvae can orient as early as 2 days post-hatch, and they swim faster and straighter as they develop. We conclude that sensory organs and swimming abilities are sufficiently developed to allow E. lori larvae to orient soon after hatch, suggesting that early orientation behavior may be common among coral reef fishes. Finally, we provide a framework for testing alternative hypotheses for the orientation strategies used by fish larvae, laying a foundation for a deeper understanding of the role of behavior in shaping dispersal patterns in the sea.
  • Nutrient and temperature constraints on primary production and net phytoplankton growth in a tropical ecosystem

    López-Sandoval, Daffne C.; Duarte, Carlos M.; Agusti, Susana (Limnology and Oceanography, Wiley, 2021-06-12) [Article]
    The Red Sea depicts a north–south gradient of positively correlated temperature and nutrient concentration. Despite its overall oligotrophic characteristics, primary production rates in the Red Sea vary considerably. In this study, based on five cruises and a 2-year time series (2016–2018) sampling in the Central Red Sea, we determined phytoplankton photosynthetic rates (PP) by using 13C as a tracer and derived phytoplankton net growth rates (μ) and chlorophyll a (Chl a)-normalized photosynthesis (PB). Our results indicate a ninefold variation (14–125 mgC m−2 h−1) in depth-integrated primary production and reveal a marked seasonality in PP, PB, and μ. Depth-integrated PP remained <30 mg C m−2 h−1 during spring and summer, and peaked in autumn–winter, particularly in the southernmost stations (~17°N). In surface waters, phytoplankton grew at a slow rate (0.2 ± 0.02 d−1), with the population doubling every 3.5 days, on average. However, during the autumn–winter period, when Chl a concentrations peaked in the central and southern regions, μ increased to values between 0.60 and 0.84 d−1, while PB reached its maximum rate (7.8 mgC [mg Chl a]−1 h−1). We used path analysis to resolve direct vs. indirect components between correlations. Our results show that nutrient availability modulates the photosynthetic performance and growth of phytoplankton communities and that PB and μ fluctuations are not directly associated with temperature changes. Our study suggests that similarly to other oligotrophic warm seas, phosphorus concentration exerts a key role in defining photosynthetic rates and the biomass levels of phytoplankton communities in the region.
  • Moderate Seasonal Dynamics Indicate an Important Role for Lysogeny in the Red Sea

    Abdulrahman Ashy, Ruba; Suttle, Curtis A.; Agusti, Susana (Microorganisms, MDPI AG, 2021-06-11) [Article]
    Viruses are the most abundant microorganisms in marine environments and viral infections can be either lytic (virulent) or lysogenic (temperate phage) within the host cell. The aim of this study was to quantify viral dynamics (abundance and infection) in the coastal Red Sea, a narrow oligotrophic basin with high surface water temperatures (22–32 °C degrees), high salinity (37.5–41) and continuous high insolation, thus making it a stable and relatively unexplored environment. We quantified viral and environmental changes in the Red Sea (two years) and the occurrence of lysogenic bacteria (induced by mitomycin C) on the second year. Water temperatures ranged from 24.0 to 32.5 °C, and total viral and bacterial abundances ranged from 1.5 to 8.7 × 106 viruses mL−1 and 1.9 to 3.2 × 105 bacteria mL−1, respectively. On average, 12.24% ± 4.8 (SE) of the prophage bacteria could be induced by mitomycin C, with the highest percentage of 55.8% observed in January 2018 when bacterial abundances were low; whereas no induction was measurable in spring when bacterial abundances were highest. Thus, despite the fact that the Red Sea might be perceived as stable, warm and saline, relatively modest changes in seasonal conditions were associated with large swings in the prevalence of lysogeny.

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