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.

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.

The evolution of oxygenic photosynthesis had profound effects on the biogeochemistry of the planet. The increase in atmospheric oxygen levels brought about alterations to a range of biogeochemical processes involving changes in the availability of a host of elements, including nitrogen, sulfur and many metal ions such as iron and manganese, central to biological activities. Critically for photosynthetic organisms, the increase in oxygen levels in the atmosphere following the evolution of oxygenic photosynthesis and the Great Oxidation Event had consequences for the assimilation of inorganic carbon via the enzyme ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco). Although there are a number of alternative pathways leading to autotrophic CO2 assimilation, 99% of primary productivity on the planet is carried out by processes that involve Rubisco and the Benson–Calvin–Bassham cycle. The accumulation of O2 in the atmosphere also had major repercussions for increasing the energetic yield of the catabolism of photosynthate by allowing oxidative respiration, with a much greater ATP yield than from anaerobic fermentative processes. The interaction of O2 with UVC radiation led to the production of UVC- and UVB-absorbing O3. This also significantly influenced life on Earth and facilitated the colonisation of the upper ocean and terrestrial surface.

The origin of life could have involved autotrophy, but this is most probably chemolithotrophic rather than photolithotrophic. There is evidence, from the natural abundance of carbon isotopes, of autotrophy involving Rubisco and the Benson–Calvin–Bassham cycle from about 4 Ga. However, other autotrophic CO2 fixation pathways could also have occurred. Evidence on the evolution of photosynthetic reactions suggests an early origin of the photochemical reaction centre, with the possibility of the occurrence of two photosystems in series (photosystem II plus photosystem I) and the possibility of oxygenic photosynthesis, before the origin of the single photosystem (reaction centre I or reaction centre II) photosynthesis in the multiple clades of anoxygenic photosynthetic bacteria. The origin of photosystem II and photosystem I preceded the origin of cyanobacteria and the subsequent Great Oxidation Event at about 2.4–2.3 Ga. The occurrence of oxygenic photolithotrophy is a necessary, but not sufficient, condition for the occurrence of the Great Oxidation Event and the Neoproterozoic Oxidation Event. There is no consensus on what other factors are involved in initiating the Great Oxidation Event and the Neoproterozoic Oxidation Event.