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Ecological data on the adult stages of marine organisms

Time and energy are finite resources in any environment, and how and when organisms use their available resources to survive and reproduce is the crux of life history theory (Gadgil and Bossert 1970; Balon 1975; Stearns 1976). The different survival strategies used by animals are often shaped by their environment in addition to their biology (Winemiller and Rose 1992), which allows for exploration into biological variability when environmental factors are known. For this reason, the Line Islands in the Central Pacific provide an ideal location to perform observational studies due to their unique productivity gradient and fish assemblage structures across the island chain (Sandin et al. 2008; DeMartini et al. 2008; Fox et al. 2018; Zgliczynski et al. 2019). Many of the world’s coral reefs are in remote regions that lack monitoring programs or even local populations, so conducting ecological surveys on fish communities in these regions can require extensive amounts of time, energy, resources and people. The inherent variability an environment exerts on the many factors that contribute to growth over a lifetime make it difficult to generate a directly proportional formula that calculates age. A novel age estimation method was developed that utilizes in-situ visual census data to estimate the age of fishes, and as a case study, several fish were chosen as representative species to explore its capabilities. Through this process, new ecological information and insight can be gained about the age structures of fish populations both between and throughout the Line Islands.

The Nekton Maldives Taxonomic Workshop took place at the Maniyafushi Research Station in the Maldives between 12 and 23 February 2023. This workshop had two primary objectives. Firstly, it aimed to identify species from biological samples and underwater imagery collected during the Nekton Maldives Mission in 2022. Secondly, it sought to facilitate training and knowledge exchange sessions between early career researchers from the Maldives and international taxonomists. These sessions were designed to share knowledge and introduce fundamental taxonomy concepts and enhance practical identification skills for common reef benthic groups and major zooplankton taxonomic groups. A total of 24 people from 10 different countries were directly or indirectly involved with the workshop comprising nine taxonomic experts, eleven trainees and four organisers. Collectively, we identified 278 biological specimens including potentially undescribed species of hydroids, black corals, sponges and octocorals, 318 morphotypes for underwater footage and zooplankton composition congruent with previous reports from the Indian Ocean Region. Next steps will involve depositing the specimens into a more a permanent facility to facilitate the process of specimen description and knowledge transfer.

Despite being an abundant group of significant ecological importance the phylogenetic relationships of the Octocorallia remain poorly understood and very much understudied. We used 1132 bp of two mitochondrial protein-coding genes, nad2 and mtMutS (previously referred to as msh1), to construct a phylogeny for 161 octocoral specimens from the Atlantic, including both Isididae and non-Isididae species. We found that four clades were supported using a concatenated alignment. Two of these (A and B) were in general agreement with the of Holaxonia–Alcyoniina and Anthomastus–Corallium clades identified by previous work. The third and fourth clades represent a split of the Calcaxonia–Pennatulacea clade resulting in a clade containing the Pennatulacea and a small number of Isididae specimens and a second clade containing the remaining Calcaxonia. When individual genes were considered nad2 largely agreed with previous work with MtMutS also producing a fourth clade corresponding to a split of Isididae species from the Calcaxonia–Pennatulacea clade. It is expected these difference are a consequence of the inclusion of Isisdae species that have undergone a gene inversion in the mtMutS gene causing their separation in the MtMutS only tree. The fourth clade in the concatenated tree is also suspected to be a result of this gene inversion, as there were very few Isidiae species included in previous work tree and thus this separation would not be clearly resolved. A~larger phylogeny including both Isididae and non Isididae species is required to further resolve these clades.

Perchlorate (ClO4-) is a toxic, water-soluble oxyanion of chlorine that is naturally and anthropogenically produced. Because of its extensive industrial uses and unregulated disposal prior to 1997, perchlorate contamination of water sources is widespread. In humans, perchlorate inhibits iodide uptake by the thyroid gland, which can lead to hypothyroidism. As a result, the Environmental Protection Agency decided to regulate perchlorate under the Safe Water Drinking Act of 2012. Dissimilatory perchlorate reducing bacteria (DPRB) can grow by respiring perchlorate (ClO4-) or chlorate (ClO3-) [collectively denoted (per)chlorate] to innocuous chloride (Cl-). Even though about 80 strains of DPRB have been isolated to date (Chapter 1), most of these isolates have been obtained from freshwater, mesophilic, neutral pH environments. As a result, most of these microorganisms do not tolerate high temperatures, salinities, or extreme pH. With few exceptions, most DPRB belong to the Alpha, Beta, Gamma and Epsilon classes of the phylum Proteobacteria. The current work aims to expand the known environmental range, metabolic strategies, and taxonomic diversity of DPRB. Shallow sediment samples from a marina in Berkeley, CA were used to study marine perchlorate reduction. Enrichments were set up at 1, 3, 5, 7, and 10% NaCl with acetate as an electron donor and perchlorate as an electron acceptor; perchlorate was consumed in salinities of up to 7% NaCl (Chapter 2). Microbial community analysis revealed that the most active members of the community were in families Rhodocyclaceae (1% and 3% NaCl), Pseudomonadaceae (1% NaCl), Campylobacteraceae (1%, 5%, and 7% NaCl), Sedimenticolaceae (3% NaCl), Desulfuromonadaceae (5% & 7% NaCl), Pelobacteraceae (5% NaCl), Helicobacteraceae (5% & 7% NaCl), and V1B07b93 (7% NaCl; phylum Deferribacteres) (Chapter 2). DPRB in the genera Sedimenticola, Azoarcus, Pseudomonas, Denitromonas, and Marinobacter (Chapter 2) were isolated. To further study the physiology and metabolic potential of marine DPRB, an Arcobacter sp. was isolated from marine sediment from the Berkeley Bay, and was fully characterized and genome sequenced (Chapter 3). Arcobacter sp. CAB is the only perchlorate reducing bacterium (PRB) in pure culture belonging to the Epsilonproteobacteria. Interestingly, CAB lacks the pcrC gene previously thought to be essential for perchlorate reduction. Additionally, CAB can couple the oxidation of the aromatic compound catechol to perchlorate reduction in anaerobic conditions. However, it utilizes an aerobic pathway that requires oxygen as a co-substrate for an oxygenase. Thus, Arcobacter sp. CAB represents the first example of a PRB that can utilize an aerobic pathway for aromatic degradation with perchlorate as an electron acceptor by utilizing oxygen produced from chlorite dismutation in otherwise anaerobic conditions. The PRB Sedimenticola selenatireducens CUZ, also isolated from Berkeley Bay sediment, and the chlorate reducing bacteria (CRB) Dechloromarinus chlorophilus NSS, isolated from San Diego Bay sediment, were fully characterized and represent the first case of two highly related microorganisms (99% 16S rRNA identity), one of which is a perchlorate-reducing bacterium (PRB) and one of which is a chlorate-reducing bacterium (CRB; Chapter 4). Both strains are metabolically versatile, and can oxidize the aromatic compounds benzoate and phenylacetate coupled to the reduction of oxygen, perchlorate, and nitrate (Chapter 5). Both strains encode aerobic-hybrid and anaerobic pathways of phenylacetate and benzoate degradation. While S. selenatireducens acts as a true anaerobe and predominantly utilizes the anaerobic pathways with perchlorate as an electron acceptor, D. chlorophilus NSS may utilize a mixture of aerobic and anaerobic pathways when respiring on chlorate (Chapter 5). The marine, perchlorate-reducing microbial community and novel isolates studied in this work greatly contribute to the current knowledge in the field of microbial perchlorate reduction. With the exception of Marinobacter, these new isolates represent the first known perchlorate-reducers in each genus (Chapter 2), thus expanding the known phylogeny of DPRB which are dominated by the genera Dechloromonas and Azospira (Chapter 1). Further, the characterization of the PRBs Arcobacter sp. CAB and S. selenatireducens CUZ and the CRB Dechloromarinus chlorophilus NSS has revealed several mechanisms by which DPRB degrade aromatic compounds and the choices these microorganisms make in respect to the oxygen they produce from the dismutation of chlorite. Further characterization and genome sequencing of the other novel DPRB obtained in this study is of great importance, and will likely aid in the study of the evolution of perchlorate metabolism and in understanding the role each of these isolates in microbial communities.

The extending record of ocean colour derived information, an important asset for the study of marine ecosystems and biogeochemistry, presently relies on individual satellite missions launched by several space agencies with differences in sensor design, calibration strategies and algorithms. In this study we present an extensive comparative analysis of standard products obtained from operational global ocean colour sensors (SeaWiFS, MERIS, MODIS-Aqua, MODIS-Terra), on both global and regional scales. The analysis is based on monthly mean chlorophyll a (Chl-a) sea surface concentration between 2002 and 2009. Based on global statistics, the Chl-a records appear relatively consistent. The root mean square (RMS) difference Δ between (log-transformed) Chl-a from SeaWiFS and MODIS Aqua amounts to 0.137, with a bias of 0.074 (SeaWiFS Chl-a higher). The difference between these two products and MERIS Chl-a is approximately 0.15. Restricting the analysis to 2007 only, Δ between MODIS Aqua and Terra is 0.142. This global convergence is significantly modulated regionally. Statistics for biogeographic provinces representing a partition of the global ocean, show Δ values varying between 0.08 and 0.3. High latitude regions, as well as coastal and shelf provinces are generally the areas with the largest differences. Moreover, RMS differences and biases are modulated in time, with a coefficient of variation of Δ varying between 10% and 40%, with clear seasonal patterns in some provinces. The comparison of the province-averaged time series obtained from the various satellite products also shows a level of agreement that is geographically variable. Overall, the Chl-a SeaWiFS and MODIS Aqua series appear to have similar levels of variance and display high correlation coefficients, an agreement likely favoured by the common elements shared by the two missions. These results are degraded if the MERIS series is compared to either SeaWiFS or MODIS Aqua. An important outcome of the study is that the results of the inter-comparison analysis are variable with time and location, and therefore globally averaged statistics are not necessarily applicable on a seasonal or regional basis.

We develop and implement a new method to take into account the impact of waves into the 3-D circulation model SYMPHONIE (Marsaleix et al., 2008, 2009a) following the simplified equations of Bennis et al. (2011) which use glm2z-RANS theory (Ardhuin et al., 2008c). These adiabatic equations are completed by additional parameterizations of wave breaking, bottom friction and wave-enhanced vertical mixing, making the forcing valid from the surf zone through to the open ocean. The wave forcing is performed by wave generation and propagation models WAVEWATCH III® (Tolman, 2008, 2009; Ardhuin et al., 2010) and SWAN (Booij et al., 1999). The model is tested and compared with other models for a plane beach test case, previously tested by Haas and Warner (2009)and Uchiyama et al. (2010). A comparison is also made with the laboratory measurements of Haller et al. (2002) of a barred beach with channels. Results fit with previous simulations performed by other models and with available observational data. Finally, a realistic case is simulated with energetic waves travelling over a coast of the Gulf of Lion (in the northwest of the Mediterranean Sea) for which currents are available at different depths as well as an accurate bathymetric database of the 0–10 m depth range. A grid nesting approach is used to account for the different forcings acting at different spatial scales. The simulation coupling the effects of waves and currents is successful to reproduce the powerful northward littoral drift in the 0–15 m depth zone. More precisely, two distinct cases are identified: When waves have a normal angle of incidence with the coast, they are responsible for complex circulation cells and rip currents in the surf zone, and when they travel obliquely, they generate a northward littoral drift. These features are more complicated than in the test cases, due to the complex bathymetry and the consideration of wind and non-stationary processes. Wave impacts in the inner shelf are less visible since wind and regional circulation seem to be the predominant forcings. Besides, a discrepancy between model and observations is noted at that scale, possibly linked to an underestimation of the wind stress. This three-dimensional method allows a good representation of vertical current profiles and permits the calculation of the shear stress associated with waves and currents. Future work will focus on the combination with a sediment transport model.

An updated comprehensive checklist of polychaete species, which have been recorded from Malaysian waters, is provided, with their geographic distributions and the research history for them. A total of 57 species belonging to 30 families have been reported since the early 1870s, with Nereididae as the most dominant family with ten species; however, more than half of the total are questionable species in the country. Despite the increased efforts of polychaete studies in the past decade, the taxonomic endeavour of discovering and describing species in the country could be higher. Malaysian polychaetes were mostly recorded from Peninsular Malaysia, whereas very few were from Borneo Island. Most previously recorded species were associated with intertidal and estuarine habitats and a few were found in the subtidal and freshwater environments. We stress the need for urgent research on this biologically, ecologically and culturally relevant taxonomic group as the species accumulation curve grows exponentially in this megadiverse country.The current checklist has been updated since the previous one in 2013. Many species previously listed were judged as doubtful and not taxonomically reliable.

Foram estudados 152 espécimes de Etmopterus capturados no levantamento pesqueiro do Projeto de Prospecção Demersal do Programa REVIZEE Score Sul, com rede de arrasto de fundo. As capturas ocorreram nos cruzeiros de inverno de 2001 e verão de 2002, na costa do Rio Grande do Sul entre o arroio Chuí (34° 20’ S) e o cabo de Santa Marta Grande (28°30’ S), nas profundidades de 100 a 600 m. As espécies capturadas foram identificadas como Etmopterus gracilispinis, E. lucifer, e E. bigelowi, e ocorreram apenas ao sul de 31° S. E. bigelowi ocorreu na faixas de profundidade de 400 a 599 m, e E. gracilispinis ocorreu na faixa de 300 a 599 m. Os dois espécimes de E. lucifer capturados, ocorreram na profundidade 540 m. As condições hidrográficas de temperatura e salinidade de fundo não apresentaram diferença sazonal, e as espécies ocorreram em fundos com sedimento síltico-argiloso. A maioria dos espécimes capturados eram imaturos, o que sugere uma segregação por faixa etária e que os adultos ocorrem em profundidades maiores que 600 m. Maturidade sexual ocorreu em E. bigelowi com comprimento total de 60 cm para os machos e com comprimento total a partir de 63 cm nas fêmeas, tendo sido capturada uma fêmea grávida no mês de agosto. Todos espécimes de E. gracilispinis eram imaturos, e um macho de E. lucifer era maturo com comprimento total de 38 cm. Foi constatado parto no mês de março para E. bigelowi e para E. gracilispinis, com comprimento total ao nascer de cerca de 17 e 13 cm, respectivamente. A total of 152 specimens of Etmopterus, were studied. This specimens were caught by bottom-trawl cruises in winter of 2001 and summer of 2002, in the Rio Grande do Sul coast between Chuí (34° 20’ S) and Santa Marta Grande Cape (28°30’ S), at depths from 100 to 600 m. The species were identified as Etmopterus gracilispinis, E. lucifer, e E. bigelowi, and occurred only at south of 31o S. E. bigelowi occurred on the deep strata from 400 to 599 m, E. gracilispinis occurred from 300 to 599 m, and the both male E. lucifer caught occurred on the depth of 540 m. The hydrographic conditions of temperature and salinity showed no seasonal differences, and the species occurred on bottoms consisting of silte and clay. Most of specimens caught were immature, what is an evidence of segregation by size and implying that the adult of these species occur at depths under 600 m. Sexual maturity appeared in E. bigelowi males of 60 cm of total length and in females starting from 63 cm of total length, having been collected a gravid female in August. All E. gracilispinis specimens were immature, and one male of E. lucifer with total length of 38 cm was mature. Was find out birth in March for E. bigelowi and for E. gracilispinis, with total length at birth of about 17 and 13 cm, respectively.

The International workshop on Atmospheric Studies in the Arctic was held at the Institute of Oceanology, Polish Academy of Sciences in Sopot, Poland on 28. and 29. January 2016. The workshop is a joint effort of the iAREA team, the Alfred Wegener Institute and the University of Florence in cooperation with the Institute of Oceanology, Polish Academy of Sciences and the Center for Polar Studies. The workshop is a contribution to the Ny-Aalesund Atmosphere Flagship Programme. This book of abstract includes the contributions building on the iAREA campaigns in 2014 and 2015 held in Ny-Aalesund, Spitsbergen.