Remote Sensing of the Aquatic Environments

The book highlights recent research efforts in the monitoring of aquatic districts with remote sensing observations and proximal sensing technology integrated with laboratory measurements. Optical satellite imagery gathered at spatial resolutions down to few meters has been used for quantitative estimations of harmful algal bloom extent and Chl-a mapping, as well as winds and currents from SAR acquisitions. The knowledge and understanding gained from this book can be used for the sustainable management of bodies of water across our planet

Is there lignin in the Ulva cell wall? A multidisciplinary structural investigation to provide new insights into cell wall evolution and macroscopic complexity in the chlorophyte green seaweeds

Seaweeds are not only an integral component of the marine ecosystem via their role in global carbon and sulfur cycles, but also have significant economic value as crops for food and fuel, with certain intertidal seaweeds like the green 'sea lettuce' Ulva (Chlorophyta) appearing as attractive bioenergy feedstocks due to their rapid growth rates and polysaccharide-rich cell wall that can comprise half its total biomass. Seaweeds have a distinct biochemistry to traditional land plant crops. For example, they lack the phenylpropanoid pathway, a key milestone in land plant evolution that enabled the biosynthesis of the secondary cell wall biopolymer lignin which confers structural support and facilitates water transport in vascular plants. Despite this, 'lignin-like' fractions are reported in Ulva, and lignin has been found in a coralline red seaweed (Rhodophyta). No alternative pathway for lignin biosynthesis is provided by our current metabolic knowledge, meaning we have limited understanding of how ‘lignin’ arose in seaweeds. Furthermore, the only comprehensive structural investigation into seaweed 'phycolignin' to date has been performed in the coralline reds. Consequently, the presence of an equivalent component in green seaweeds like Ulva is still debatable. As the primary aim of this thesis, I investigate the identity of the proposed lignin-like fraction of Ulva using confocal microscopy, biochemical assays, and biophysical analysis. To accomplish this, I evaluate the use of a sequential extraction protocol described for charophyte green algae (Streptophyta) to determine which cell wall polysaccharides the proposed structure associates with. No evidence for lignin-like structures in the Ulva cell wall was identified during this research. Instead, I propose that the previous attributions to lignin in Ulva were misidentifications on account of the limitations of quantification protocols used. Interestingly, a major structural protein component is identified with possible implications for how Ulva mitigates osmotic stress at low tide. The absence of 'phycolignin' in the Ulva cell wall contrary to the lignified coralline seaweeds demonstrates that seaweeds display diverse adaptations to intertidal habitats, and provides support to the current hypothesis that lignin arose convergently in the red lineage, with green seaweeds and land plants sharing a more recent evolutionary history

Seaweed diversity in Vietnam, with an emphasis on the brown algal genus Sargassum

Vietnam, a country in South-East Asia, is characterized by a coastline nearly 3300 km long. The coast; stretching from Gulf of Tonkin in the North to the gulf of Thailand in the South, has a predominant North-South orientation resulting in a rich and varied coastal environment. The people in Vietnam have traditionally relied on the rich coastal resources, first by harvesting natural populations and more recently by implementing aquaculture practices. Next to fish and shellfish, marine seaweeds (macroalgae) have traditionally been harvested among most of the Vietnamese coast. A survey of the uses of Vietnamese seaweeds results in 82 species which are considered economically valuable (Chapter 1). Many of these seaweeds are used for human consumption, while others have a role in traditional medicine or are used for colloid extraction (e.g. agar, carrageenan) or as feed for animals. Contrary however to neighboring countries such as China, the Philippines and Indonesia where seaweed mariculture has been seriously developed over the last decades, culturing seaweeds remains a largely marginal activity in Vietnam. Reasons as to why seaweed mariculture has not taken off as compared to the neighboring countries are at least partly to be found in the absence of a phycolloid industry in Vietnam. Instead Vietnam exports large amounts of raw seaweeds, harvested from natural populations, at a low price, and then imports the purified phycocolloids at a much higher price. A steadily growing demand for seaweed-derived products results in an increasing pressure on coastal ecosystems which risk overharvesting of natural populations. This risk is especially eminent for the brown algal genus Sargassum of which approximately 50.000 wet tons is harvested every year. Sargassum represents an important ecosystem engineering species of subtidal coastal habitats. The plants can grow easily up to 3-4 m in length and form dense vegetations with a major nursery function for countless juvenile vertebrate and invertebrate species. If plants, the uprights at least are annual, are harvested before becoming fertile, this may reduce the rejuvenation of natural populations and eventually lead to habitat degradation. Despite the value of seaweeds for humans as well as their role in coastal ecosystems in Vietnam, relatively little is known about them. Basic information on for example the number of species present and their distributions is not easily available. Most information on seaweeds is scattered in local literatures, written in Vietnamese. Thereto, we compiled a checklist of Vietnamese seaweeds (Chapter 2). A total of 827 species are reported (412 Rhodophyta, 180 Chlorophyta, 147 Phaeophyceae, 88 Cyanobacteria. This species richness is comparable to that of the Philippines and considerably higher than Taiwan, Thailand or Malaysia. A comparison of the species composition with neighbouring countries yielded surprisingly low similarities. Rather than an indication of a biogeographical pattern, we are of the opinion that the low similarity with neighboring countries is primarily an artifact resulting from taxonomic inconsistencies. The checklist could serve as a valuable tool, to reveal the seaweed diversity in Vietnam and to stimulate intraregional comparative research. Sargassum with 70 species and intraspecific taxa is undoubtedly the most species-rich seaweed genus in Vietnam (Chapter 3). The estimate of Sargassum diversity is however entirely based on interpretations of the morphological characters such as the base, secondary axes, the leaves, vesicles and receptacles. Therefore we reassessed Sargassum diversity based on molecular gene sequence data of the internal spaces of the ribosomal cistron (ITS rDNA) (Chapter 4). Although successful at higher taxonomic levels, subgenera and sections, the resolution of the ITS marker was not sufficient to point species boundaries with confidence. Many morphologically distinct ‘species’ were characterized by virtually identical ITS sequences. Conversely, specimens identified on morphological criteria as one ‘species’ were resolved in different clades. Results could be interpreted in two possible ways. First, traditional species concepts in Sargassum have been too broadly defined and the genus contains far less species. Alternatively, species in Sargassum result from a recent radiation and even the highly variable ITS region does not display enough variation to resolve the relationship among them. To address these outstanding questions we explored to use of Restriction site Associated DNA Sequences (RAD-Seq) to generate a set of highly variable nuclear markers. RAD-sequencing is a Next Generation Sequencing-based technique that generates thousands to hundreds of thousands DNA fragments that can be scored for Single Nucleotide Polymorphisms (SNPs) which in turn can be compared between individuals. RAD markers can be used to pinpoint loci under selection, or are used as neutral markers to reconstruct phylogeographical patterns or elucidate phylogenetic relationships among closely related species. During the experiment we generated more than 21 million sequences which after quality control and analyses in Stacks and SiLiX yielded 231 alignments which could potentially be used to address species boundaries in the genus Sargassum. The development of more than 200 markers presents a more than significant increase over markers used in traditional studies which generally combine one or two mitochondrial and/or chloroplast markers with sequences from the ribosomal cistron. It also boosts the number of potential markers by a factor 10 to 20 compared to microsatellite-based studies. Despite these results, there are issues that remain to be solved. For example, the libraries of the individual specimens are highly unequal in size. Some specimens are represented by 1.5 million sequences while others only have barely 800 sequences. We believe the main reason why some specimens are underrepresented is due to insufficient DNA quality. Therefore, future studies should focus on obtaining high quality DNA from Sargassum. A second issue is posed by the presence of multiple alleles in the final alignments. Normally one would expect 2 alleles per marker for a diploid organism. Our final alignments often contain more than 2 alleles per specimen. It is unclear at present if this is a technical issue which could eventually be solved by fine-tuning the parameters of the Stacks analyses or whether the multiple alleles issue has an underlying biological cause (polyploidisation). Despite these issues, RAD Sequencing has a great potential for population based molecular studies in algae. A selection of the current stacks can be used for primer design which can then be used to score markers by PCR followed by traditional Sanger sequencing. This approach can easily increase the number of nuclear markers for phylogeographic or species delimitation studies by a factor ten. Modest as it may be, I hope that by providing a compilation of the seaweed diversity in Vietnam and their economical importance, and by introducing DNA-based methodologies to assess species diversity in the ecologically and economically important genus Sargassum, I have contributed to the foundation for a sustainable exploitation of natural resources and continuous integrity of marine habitats

Ulva growth, development and applications

The green marine macroalgae Ulva (Ulvophyceae) are common algae distributed worldwide, which play a key role in aquatic ecosystems. Ulva species are a potentially valuable resource for food, feed, fertiliser and fuel but can also cause massive nuisance blooms if they grow unchecked. For correct growth and development, Ulva requires the presence of a combination of regulatory morphogenetic compounds released by associated epiphytic bacteria in addition to nutritional parameters. The first results chapter examines the extent of specificity or generality of bacteria-induced morphogenesis in Ulva, by cross-testing bacteria isolated from several Ulva species on Ulva mutabilis and Ulva intestinalis. We show that pairs of bacterial strains isolated from Ulva species can fully rescue U. mutabilis or U. intestinalis morphology. In the second results chapter, activity of algal growth- and morphogenesis-promoting factors (AGPFs) derived from bacteria were estimated in a land-based integrated multitrophic aquaculture system (IMTA) of fish and macroalgae (located at the coastal lagoon Ria de Aveiro, Portugal), using a standardised bioassay with axenic cultures of Ulva. Nutrient availability was also assessed in this IMTA system. The study thus informs aspects of the various potential aquaculture-environment interactions. It was observed that both the water from the lagoon (external to the farm system) and the water from the fish pond (input for algae cultures) could completely restore the normal growth and morphology of the macroalga under axenic conditions. The results highlight the presence of a sufficient chemical cocktail of AGPFs in this IMTA system required for growth and morphogenesis of Ulva. In addition, the water of fish farming increases the nutrient availability (nitrate and ammonium) needed for macroalgae production. The conclusion of this chapter is that Ulva´s sustainable growth and development can benefit from multitrophic aquaculture systems and shallow water systems, due to the naturally enriched AGPFs and their in-situ production by bacteria in intensive algal aquacultures. In the final results chapter, the effects of U. intestinalis extracts on germination and root development in the model land plant Arabidopsis thaliana were examined. Ulva extract concentrations above 0.1% inhibited Arabidopsis germination and root growth. Ulva extract <0.1% stimulated root growth. All concentrations of Ulva extract inhibited lateral root formation. An abscisic-acid insensitive mutant showed altered sensitivity to germination- and root growth-inhibition. Ethylene- and cytokinin-insensitive mutants were partly insensitive to germination-inhibition. This suggests that different mechanisms mediate each effect of Ulva extract on early Arabidopsis development and that multiple hormones contribute to germination-inhibition. Taken together, the results of this thesis highlight: (i) Specific Ulva-associated bacterial functions (promoting cell division, or cell differentiation) that cannot be assigned to a specific genus/taxonomic group of bacteria, (ii) an IMTA system ensuring an adequate supply of nutrients and a sufficient chemical mixture of AGPFs for reliable Ulva cultivation and (iii) the first-characterised mechanisms to date by which Ulva extract can impact germination and growth in Arabidopsis

BRIDGING FUNCTIONAL AND PHYLOGENETIC DIVERSITY OF MARINE HETEROTROPHIC PROTISTS VIA SINGLE-CELL TRANSCRIPTOMICS

The comprehensive description of unicellular heterotrophic protists is essential for understanding the functioning of marine ecosystems and defining evolutionary relationships within marine microbial communities. For that reason, new insights into the functional genes of key protists, such as ciliates and dinoflagellates, are needed to complement the increasing taxonomic complexity and bridge the gap between various eco-functional processes in the ocean. In this study, single-cell transcriptomic sequencing proved to be an efficient method to create a snapshot of expressed genes of unicellular heterotrophs. We sequenced 65 single-cell transcriptomes from 20 fresh field samples collected from Sub-Arctic and North Sea waters. These 13 ciliate and 52 dinoflagellate transcriptomes will generally contribute to a greater understanding of functional and evolutionary processes of these marine protists. Further, we generated multi-gene phylogenies of several dozen genes to unravel the relationships of these heterotrophic taxa to other dinoflagellates and ciliates, respectively. These approaches also helped to elucidate the evolution of functional genes and traits for these understudied essential groups. Additionally, the datasets were incorporated into our metatranscriptomic reference database to fill the gap (of approx. 50%) of genomic information of heterotrophic organisms and their functional processes. Overall, identifying the phylogenetic relationships and functional diversity of heterotrophic and mixotrophic protists will clarify paramount marine microbial food web processes and provide clues to the system's sensitivity to climate change

Prediction and optimisation of fuel consumption for inland ships considering real-time status and environmental factors

The information about ships’ fuel consumption is critical for condition monitoring, navigation planning, energy management and intelligent decision-making. Detailed analysis, modelling and optimisation of fuel consumption can provide great support for maritime management and operation and are of significance to water transportation. In this study, the real-time status monitoring data and hydrological data of inland ships are collected by multiple sensors, and a multi-source data processing method and a calculation method for real-time fuel consumption are proposed. Considering the influence of navigational status and environmental factors, including water depth, water speed, wind speed and wind angle, the Long Short-Term Memory (LSTM) neural network is then tailored and implemented to build models for prediction of real-time fuel consumption rate. The validation experiment shows the developed model performs better than some regression models and conventional Recurrent Neural Networks (RNNs). Finally, based on the fuel consumption rate model and the speed over ground model constructed by LSTM, the Reduced Space Searching Algorithm (RSSA) is successfully used to optimise the fuel consumption and the total cost of a whole voyage

Ocean carbon from space: Current status and priorities for the next decade

The ocean plays a central role in modulating the Earth’s carbon cycle. Monitoring how the ocean carbon cycle is changing is fundamental to managing climate change. Satellite remote sensing is currently our best tool for viewing the ocean surface globally and systematically, at high spatial and temporal resolutions, and the past few decades have seen an exponential growth in studies utilising satellite data for ocean carbon research. Satellite-based observations must be combined with in-situ observations and models, to obtain a comprehensive view of ocean carbon pools and fluxes. To help prioritise future research in this area, a workshop was organised that assembled leading experts working on the topic, from around the world, including remote-sensing scientists, field scientists and modellers, with the goal to articulate a collective view of the current status of ocean carbon research, identify gaps in knowledge, and formulate a scientific roadmap for the next decade, with an emphasis on evaluating where satellite remote sensing may contribute. A total of 449 scientists and stakeholders participated (with balanced gender representation), from North and South America, Europe, Asia, Africa, and Oceania. Sessions targeted both inorganic and organic pools of carbon in the ocean, in both dissolved and particulate form, as well as major fluxes of carbon between reservoirs (e.g., primary production) and at interfaces (e.g., air-sea and land–ocean). Extreme events, blue carbon and carbon budgeting were also key topics discussed. Emerging priorities identified include: expanding the networks and quality of in-situ observations; improved satellite retrievals; improved uncertainty quantification; improved understanding of vertical distributions; integration with models; improved techniques to bridge spatial and temporal scales of the different data sources; and improved fundamental understanding of the ocean carbon cycle, and of the interactions among pools of carbon and light. We also report on priorities for the specific pools and fluxes studied, and highlight issues and concerns that arose during discussions, such as the need to consider the environmental impact of satellites or space activities; the role satellites can play in monitoring ocean carbon dioxide removal approaches; economic valuation of the satellite based information; to consider how satellites can contribute to monitoring cycles of other important climatically-relevant compounds and elements; to promote diversity and inclusivity in ocean carbon research; to bring together communities working on different aspects of planetary carbon; maximising use of international bodies; to follow an open science approach; to explore new and innovative ways to remotely monitor ocean carbon; and to harness quantum computing. Overall, this paper provides a comprehensive scientific roadmap for the next decade on how satellite remote sensing could help monitor the ocean carbon cycle, and its links to the other domains, such as terrestrial and atmosphere

Modelling the Seasonal Growth of the Brown Seaweed Fucus Vesiculosus in the Kiel Outdoor Benthocosms

Warming and acidification of the oceans as a consequence of increasing CO2-concentrations occur globally. In mesocosm experiments, the single and combined impact of elevated seawater temperature and pCO2 (1,100 ppm) on the brown alga Fucus vesiculosus together with its ssociated community (epiphytes and mesograzers) was studied in four consecutive experiments (from April 2013 to April 2014). Based on these experiments, a numerical boxmodel simulating the seasonal growth of F. vesiculosus in the Kiel Outdoor Benthocosms (KOBs) was developed. Nitrogen and carbon cycling in the KOBs were considered and relevant physiological and ecological processes were implemented. To run simulations under present and global change scenarios (e.g. warming, ocean acidification) the model was forced with atmospheric and hydrographic data of the Kiel fjord. DIN and DIC concentration in the water and Fucus growth as carbon and nitrogen increase were explicitly modelled. For instance, the following processes were implemented: (1) Storage of carbon and nitrogen assimilates by Fucus, leading to a temporal decoupling of assimilation and growth. (2) Shading effects of epiphytes. (3) Grazing by Idotea, Gammarus and Littorina on both Fucus and epiphytes, but with species-specific rates and preferences. At present, the model is a suitable scientific tool capable of integrating our knowledge about macroalgal processes, their growth and productivity in coastal areas. It further facilitates the communication of complex knowledge to lay persons. Ultimately, the development of a predictive model, which can be coupled to a 3D-high resolution western Baltic Sea model, is anticipated. This will allow observations on the consequences of global change for the wellbeing and distribution of F. vesiculosus in the western Baltic Sea. Understanding responses of macroalgae and of the associated community is important because changing global temperatures and elevated CO2 may affect the ecological role of Fucus as primary producer, carbon sink, water purifier, and ecosystem engineer in the coastal ecosystem of the Baltic Sea

Ocean carbon from space: Current status and priorities for the next decade

The ocean plays a central role in modulating the Earth\u27s carbon cycle. Monitoring how the ocean carbon cycle is changing is fundamental to managing climate change. Satellite remote sensing is currently our best tool for viewing the ocean surface globally and systematically, at high spatial and temporal resolutions, and the past few decades have seen an exponential growth in studies utilising satellite data for ocean carbon research. Satellite-based observations must be combined with in-situ observations and models, to obtain a comprehensive view of ocean carbon pools and fluxes. To help prioritise future research in this area, a workshop was organised that assembled leading experts working on the topic, from around the world, including remote-sensing scientists, field scientists and modellers, with the goal to articulate a collective view of the current status of ocean carbon research, identify gaps in knowledge, and formulate a scientific roadmap for the next decade, with an emphasis on evaluating where satellite remote sensing may contribute. A total of 449 scientists and stakeholders participated (with balanced gender representation), from North and South America, Europe, Asia, Africa, and Oceania. Sessions targeted both inorganic and organic pools of carbon in the ocean, in both dissolved and particulate form, as well as major fluxes of carbon between reservoirs (e.g., primary production) and at interfaces (e.g., air-sea and land–ocean). Extreme events, blue carbon and carbon budgeting were also key topics discussed. Emerging priorities identified include: expanding the networks and quality of in-situ observations; improved satellite retrievals; improved uncertainty quantification; improved understanding of vertical distributions; integration with models; improved techniques to bridge spatial and temporal scales of the different data sources; and improved fundamental understanding of the ocean carbon cycle, and of the interactions among pools of carbon and light. We also report on priorities for the specific pools and fluxes studied, and highlight issues and concerns that arose during discussions, such as the need to consider the environmental impact of satellites or space activities; the role satellites can play in monitoring ocean carbon dioxide removal approaches; economic valuation of the satellite based information; to consider how satellites can contribute to monitoring cycles of other important climatically-relevant compounds and elements; to promote diversity and inclusivity in ocean carbon research; to bring together communities working on different aspects of planetary carbon; maximising use of international bodies; to follow an open science approach; to explore new and innovative ways to remotely monitor ocean carbon; and to harness quantum computing. Overall, this paper provides a comprehensive scientific roadmap for the next decade on how satellite remote sensing could help monitor the ocean carbon cycle, and its links to the other domains, such as terrestrial and atmosphere