Over 70% of the Earth’s surface is covered by saline environments. While the salinity of the open ocean is fairly stable, in coastal waters and estuaries, where river freshwater mixes with marine water bodies, salinity is usually highly variable, and, in some situations, such as lagoons or rock pools, evaporation of water can lead to hypersaline conditions. Changes in salinity directly affect water potential and turgor pressure in walled cells. Furthermore, salinity changes alter the intracellular concentration of inorganic ions such as sodium, which can have deleterious effects on processes such as photosynthesis and respiration. Salinity can therefore pose challenges for the physiology and growth of aquatic phototrophs. Algae respond to differences in salinity through a range of physiological mechanisms, including osmotic adjustment involving inorganic ion fluxes and the production of organically compatible solutes. In some cases, acclimation to salinity involves ultrastructural plasticity. Horizontal salinity gradients, found in environments including estuaries, lagoons or semi-isolated systems such as the Baltic Sea, promote the development of physiologically distinct variants of algal species, known as ecotypes, and eventually speciation in algae.

Solar radiation is the major factor shaping the environment where algae, cyanobacteria and aquatic macrophytes can thrive. Light is the energy source for photosynthesis and growth and can control algal net primary production. Changes in light intensity occur on orders of magnitude within timescales from milliseconds to hours, seasons and even eons. In water, light is exponentially attenuated with depth, with attenuation being wavelength dependent. As a result, the intensity and spectrum of available light can be very dynamic and unpredictable. To cope with such a challenging environment, an array of sensing and feedback-loop mechanisms has evolved in aquatic phototrophs. The structural and functional plasticity of light harvesting and photoprotection mechanisms is also extremely high. This has allowed algae to occur, thrive and evolve in all niches where light is available.

Microalgae, with cyanobacteria, are the major primary producers in aquatic, predominantly marine, ecosystems, contributing to the biogeochemical cycling of multiple elements despite their small instantaneous biomass. Their evolutionary history revealed by genomic analyses has shown a complex past that produces a polyphyletic group including organisms that have undergone primary, secondary and tertiary chloroplast endosymbiosis with genetic integration and also horizontal gene transfer. All but one genus of photosynthetic eukaryotes arose by endosymbiosis of a gloeomargarita-like β-cyanobacterium in a eukaryote with the retention of some genes in the plastid, the transfer of more genes to the eukaryote nucleus, and the loss of many others, to produce the Archaeplastida. A second, much later, endosymbiosis of an α-cyanobacterium in a euglyphid amoeba yielded Paulinella. The diversification of the Archaeplastida yielded Glaucophyta, Rhodophyta, Chlorophyta and Streptophyta. Secondary endosymbiosis of red algae in eukaryotes led to microalgae of the ‘red line’, that is, photosynthetic Ochrista (= stramenopiles), Haptophyta, Cryptophyta and Alveolata (dinoflagellates and chromerids). Secondary endosymbiosis of chlorophyte algae in eukaryotes yielded microalgae of the Chlorarachniophyta and Euglenophyta. The ‘red line’ of secondary endosymbionts are dominant marine phytoplankton, possibly related to the occurrence of chlorophyll c that has high absorbance of blue light that dominates in deep ocean waters.

Aquatic phototrophs are increasingly being exposed to a host of potentially toxic materials, mostly anthropogenic in origin, that contaminate oceans and freshwater ecosystems. Here, focusing on algae, we consider the effects of pesticides (herbicides and insecticides), polychlorinated biphenyls, plastics, hydrocarbons and heavy metals on aspects of growth and physiological performance. Algae differ widely in their resistance to these pollutants, but some have been shown to actively remove toxicants from the surrounding water, either by biochemical detoxification processes or by absorption to cell components (in many cases the cell wall). Algae with the ability to remove pollutants from affected water have been proposed as possible agents of bioremediation, though to date most of the studies have been at the laboratory scale and there is a need to show that algal remediation can be achieved at scale. There is also a need for more studies using ecologically relevant concentrations of pollutants and investigation of interactions between multiple pollutants and environmental factors.

The major essential nutrients, nitrogen and phosphorus, limit primary productivity in many aquatic environments, though in some areas of the ocean (high nutrient low chlorophyll), productivity is limited by the availability of iron or iron and manganese. Planktonic cyanobacteria are major nitrogen fixers in marine and fresh waters; heterocystous cyanobacteria are common in fresh waters and occur as symbionts in marine diatoms. Non-heterocystous marine cyanobacteria occur free-living and as algal symbionts. Nitrogen fixation requires iron and molybdenum, which can be less commonly replaced by vanadium, as well as reductants and ATP. For combined nitrogen, the form assimilated into organic nitrogen is, as for diazotrophs, ammonium, which is taken up by specific transporters. Nitrate influx also involves an energised transporter. Nitrate reductase requires catalytic iron and molybdenum and reductant to produce nitrite; nitrite is reduced to ammonium by nitrite reductase using catalytic iron. Several forms of organic nitrogen can also be taken up and assimilated by algae. Phosphorus is taken up as inorganic phosphate; organic phosphate from the medium is hydrolysed by phosphatases secreted by algae. Aquatic rhizophytic macrophytes with rhizoids or roots in fine-grained substrates acquire various fractions of combined nitrogen and of phosphate from the sediment and from overlying water.

Aquatic phototrophs have a remarkable ability to cope with variations in a range of environmental factors, such as light, temperature, pH and salinity. However, some environmental conditions are beyond what are considered the normal limits for growth and can thus be considered as extreme. Focusing on algae and cyanobacteria, we discuss the capacity of extremophilic organisms to cope and even thrive in extremes of temperature ranging from hot springs to snow and ice algae, under extremes of pH and in situations where water is in short supply, such as in biological soil crusts and on man-made surfaces such as buildings and statues. Many of the mechanisms that allow algae to cope with these extremes are common across different situations and involve, for instance, processes to dissipate excess light energy and deal with reactive oxygen species. Algae and cyanobacteria enter symbiotic associations with other organisms, such as lichens and corals. They are also found as intracellular symbionts in plants, other algae and various protists and metazoans. There are looser associations where algae grow on animals such as gastropods, seals and terrestrial animals such as sloths. We also discuss the retention of active chloroplasts by phagotrophs in the process of kleptoplasty.

Increases in atmospheric CO2 expected over the next century will cause further global warming and further increases in the CO2 concentration in water bodies and, by equilibration of CO2 with HCO3− - CO32− - H+, increased HCO3− and H+ and decreased CO32−. Warming increases stratification and shoaling of the thermocline; this decreases the supply of nutrients regenerated in deep waters to the upper mixed layer across the thermocline, and increases mean photosynthetically active and UV radiation in the upper mixed layer. Taken separately, these changes can have profound changes on the performance of algae and, because of differences among taxa, in the species composition of primary producer populations. However, it is becoming increasingly clear that the effects of individual components of global change cannot be used as useful predictors of what will happen to aquatic ecosystems into the future and that studies need to take more cognisance of the interactive effects between such factors. There is evidence for genetic adaptation, as well as phenotypic acclimation, in algae exposed to either elevated CO2 or increased temperature. Our understanding of the effects on global change requires further studies into the genetic and acclimation responses of algae exposed to combinations of changed environmental factors.

Mixoplankton are planktonic protists engaging in photo-autotrophy plus osmo-heterotrophy plus phago-heterotrophy, contrasting with non-phagotrophic phytoplankton (e.g., diatoms) and non-phototrophic zooplankton (e.g., tintinnids). All mixoplankton are mixotrophs, but not all mixotrophs are mixoplanktonic. Mixoplankton are often considered as inferior in their capabilities compared to diatoms that surrendered phagotrophy, and those zooplankton that lost phototrophy. However, such views undersell the synergistic activities of mixoplankton. Thus, the phototrophic capacity of mixoplankton provides a predatory phagotroph with a ready source of carbon and energy supplementing phagotrophy and retention of the 30% of resources that would otherwise have to be released in specific dynamic action. Phagotrophy brings in nutrients to support phototrophy. Beyond these generalisations, we know little about the whole integrated physiology and ecology of mixoplankton. To fully appreciate the comparative fitness of two species, we need to consider all aspects of their life cycles. The emphasis for plankton is usually placed on resource acquisition and the maximum specific growth rate without considering the metabolic and mortality costs of being unable to support the growth rate, and predatory pressures. This suggests that trait trade-offs are less useful for conceptual and simulation modelling than approaches more securely founded in physiology and evolution.

Photosynthesis evolved in the Archean. Before the Great Oxidation Event, the dominant form of photosynthesis was anoxygenic bacterial photosynthesis, although there is molecular phylogenetic evidence of the occurrence of oxygenic cyanobacteria (or their ancestors) in the Archean, explaining the occurrence of ‘whiffs of oxygen’ in the Archean. Recent molecular genetic evidence shows that phototrophy is a synapomorphy of only one of the six clades of anoxygenic phototrophs (the Chlorobi) and of the oxygenic cyanobacteria, so the occurrence of phototrophy in the other five clades of anoxygenic phototrophy involves horizontal gene transfer. Photolithotrophy only occurs in three clades of anoxygenic bacteria, that is, the Chlorobi with reaction centre I for photochemistry and the reverse tricarboxylic acid cycle for CO2 fixation, the Chloroflexi with reaction centre II for photochemistry and the 3-hydroxypropionate bi-cycle or the Benson–Calvin–Bassham cycle for CO2 fixation, and the γ-proteobacteria with reaction centre 2 for photochemistry and the Benson–Calvin–Bassham cycle for CO2 fixation. The oxygenic cyanobacteria have photosystem I (homologue of reaction centre I) and photosystem II (homologue of reaction centre II) in linear electron flow, and photosystem I in cyclic electron flow, and the Benson–Calvin–Bassham cycle for CO2 fixation.

Unicellular phototrophs inhabit ecological niches ranging from extremely cold environments in polar or glacier regions to hot springs. This extremely broad spectrum of temperature tolerance is the consequence of specific adaptation responses acquired during evolution. The molecular mechanisms required to maintain high physiological activity under natural temperature conditions are not completely understood. Temperature adaptation in phototrophs is an important issue in algal biotechnology, as well as in climate prediction, because the algal response to an increased earth surface temperature strongly influences the global carbon budget. In this chapter, the mechanisms of temperature acclimation are summarised to identify potential targets for biotechnology or for improved climate prediction.

Nutrients, frequently phosphorus and/or nitrogen, often limit aquatic primary productivity. The availability of nutrients required by phototrophs varies with chemical and biological species, site and season. A rapidly increasing, resource-demanding human population that uses water as a convenient waste-disposable system has caused widespread nutrient pollution leading to ‘eutrophication’. In conjunction with other multiple pressures such as climate change, this has altered the natural communities in an ecosystem, and caused biodiversity loss. It also causes a cascade of undesirable consequences for human use of water, including the growth of potentially toxic microalgal and macroalgal blooms, and deoxygenation leading to fish kills and the release of nutrients from the sediment to the water. Remediation, driven by legislation, is focused on limiting nutrient losses from agricultural systems while maintaining the ability to produce food sustainably and increasing nutrient capture in works treating domestic and industrial waste and the production of a circular economy for nutrients.

Seagrasses in marine systems and freshwater plants (macrophytes) in inland waters are important primary producers that structure their local ecosystems. They comprise the embryophytes: bryophytes, pteridophytes and angiosperms. They have adapted the genetic heritage of their land plant ancestors in response to the opportunities and challenges of life underwater. This has involved a reduction in the structures and processes required to manage: water content, the low physical support in air and the high levels of UV radiation. In contrast, inorganic carbon can restrict photosynthesis underwater but can be minimised by growing in sites with high CO2 concentrations, exploiting CO2 in the air or sediment and by CO2 concentrating mechanisms that rely on bicarbonate uptake, C4 photosynthesis or Crassulacean acid metabolism. Most aquatic embryophytes are, like their terrestrial ancestors, rhizophytic, allowing nutrients to be taken up from both the sediment and water. Some, especially the bryophytes, are haptophytic and only obtain nutrients from the water column.

Multicellularity among algae is not restricted to macroalgae, nor are all macroalgae multicellular. Multicellularity contrasts with colonies of identical cells by differentiation of cell types and intercellular connections; by this definition, heterocystous cyanobacteria are multicellular, as are some freshwater green algae in the streptophyte and chlorophyte lineages. Multicellular, mainly marine, macroscopic algae include Rhodophyta and Phaeophyceae. Among large marine chlorophytan green algae, Ulva has no plasmodesmata, while differentiated Ulvophyceae, such as Acetabularia, Caulerpa, Halimeda and Codium, are composed of a single cell, demonstrating that organ growth and morphogenesis are independent from cell division, so the most complex green seaweeds are both macroscopic and unicellular/acellular. Macroscopic seaweeds of the Rhodophyta, Chlorophyta and Phaeophyceae clades arose from small unicellular ancestors, with the red and green lineages dating back most likely to the Meso- or Neoproterozoic (1,600–900 Ma) and brown seaweeds to about 200 Ma. Compared to benthic microalgae, macroalgae project beyond the substrate boundary layer, but have their own diffusion boundary layer constraining nutrient acquisition, and have more self-shading of photosynthetically active radiation than do individual microalgal cells. These constraints are partly offset by wave activity.

In addition to the current uses of algae as food and as sources of pigments and polysaccharides, there is potential for the further use of algae as sources of additional specific biomolecules. In addition to this, there is the possibility of the use of alga in a wide variety of processes such as bioenergy (production of liquid fuels and algal biophotovoltaic generation of electricity), removing pollutants from wastewater, and the production of plant growth enhancers and crop protection materials. The eventual commercialisation of these requires the processes to be scalable and economical. The targeted use of algae, other than as food sources, is less than 100 years old and our knowledge of algal biology, physiology and chemistry is still growing and only a very small number of algal species have been studied in detail. One of the main limitations is the need for more reliable, lower cost and larger-scale algae production systems and their development, in turn, requires a good understanding of basic algal biology and life histories. In addition, more work is needed on increasing the efficiency of light utilisation in photosynthesis and hence in growth.