About 40 years have passed since the discovery of picophytoplankton; the present knowledge of the taxonomy physiology and ecology of these tiny photoautotrophic cells offers new perspectives on the importance of the microbial contribution to global biogeochemical cycles and food webs. This review focuses on the relationships among the components of picophytoplankton (picocyanobacteria and the picoplanktic eukaryotes) and biotic and abiotic environmental factors. The dynamics of picophytoplankton in aquatic ecosystems are strictly dependent upon basin size and trophy, temperature, and nutrient and light limitation, but they are also regulated by grazing and viral-induced lysis. The review considers: the pros and cons of the molecular approach to the study of the taxonomy of freshwater Synechococcus spp.; the importance of ecological aspects in understanding the puzzle of picophytoplankton phylogeny (genotype vs ecotype); and the role of biotic vs abiotic interactions in controlling picophytoplankton dynamics. Biotic, top-down control mechanisms are reviewed as well as knowledge of other biological interactions.

The European Water Framework Directive requires member states to restore aquatic habitats to good ecological status (quality) by 2015. Good ecological status is defined as slightly different from high status, which, according to the Directive, means negligible human influence. This poses problems enough for restoration of natural habitats but artificial reservoirs are not excluded from the Directive. They must be restored to good ecological potential. The meaning of good ecological status is linked to that of ‘high’ ecological status, the pristine reference condition for aquatic habitats under the Directive. From the point of view of an ecologist, this is taken to mean the presence of four fundamental characteristics: nutrient parsimony, characteristic biological and physical structure, connectivity within a wider system and adequate size to give resilience of the biological communities to environmental change. These characteristics are strongly interrelated. Ecological potential must bear some relationship to ecological status but since the reference state for ecological quality is near absence of human impact, it is difficult to see how the criteria for ecological status can be applied to a completely man-made entity where the purpose of the dam is deliberately to interfere with the natural characteristics of a river or former natural lake. Reservoirs are disabled lakes, usually lacking the diversity and function provided by a littoral zone. Nonetheless, pragmatic approaches to increasing the biodiversity of reservoirs are reviewed and conclusions drawn as to the likely effectiveness of the legislation.

In most lakes, zooplankton production is constrained by food quantity, but frequently high C:P poses an additional constraint on zooplankton production by reducing the carbon transfer efficiency from phytoplankton to zooplankton. This review addresses how the flux of matter and energy in pelagic food webs is regulated by food quantity in terms of C and its stoichiometric quality in terms of C:P. Increased levels of light, CO₂ and phosphorus could each increase seston mass and, hence, food quantity for zooplankton, but while light and CO₂ each cause increased C:P (i.e. reduced food quality for herbivores), increased P may increase seston mass and its stoichiometric quality by reducing C:P. Development of food quality and food quantity in response to C- or P-enrichments will differ between ‘batch-type’ lakes (dominated by one major, seasonal input of water and nutrients) and ‘continuous-culture’ types of lakes with a more steady flow-rate of water and nutrients. The reciprocal role of food quantity and stoichiometric quality will depend strongly on facilitation via grazing and recycling by the grazers, and this effect will be most important in systems with low renewal rates. At high food abundance but low quality, there will be a ‘quality starvation’ in zooplankton. From a management point of view, stoichiometric theory offers a general tool-kit for understanding the integrated role of C and P in food webs and how food quantity and stoichiometric quality (i.e. C:P) regulate energy flow and trophic efficiency from base to top in food webs.

We have reviewed the phytoplankton composition and succession in the East African Great Lakes, their response to environmental changes, and the communities of microorganisms of the microbial food web. Recent studies in some great lakes, as well as progress in understanding phytoplankton succession and response to environmental factors, enable us to update knowledge of the phytoplankton ecology of these lakes. In particular, we present information indicating that phytoplankton composition in lakes Tanganyika and Kivu may reflect recent changes as a result of global warming or species introduction. We also stress the importance of microbes (at the base of the food web) in these systems and suggest that the microbial food web, which has been mostly overlooked until recently, may play a very large role in determining productivity and nutrient cycling in these large lakes.

River structure and functioning are governed naturally by geography and climate but are vulnerable to natural and human-related disturbances, ranging from channel engineering to pollution and biological invasions. Biological communities in river ecosystems are able to respond to disturbances faster than those in most other aquatic systems. However, some extremely strong or lasting disturbances constrain the responses of river organisms and jeopardise their extraordinary resilience. Among these, the artificial alteration of river drainage structure and the intense use of water resources by humans may irreversibly influence these systems. The increased canalisation and damming of river courses interferes with sediment transport, alters biogeochemical cycles and leads to a decrease in biodiversity, both at local and global scales. Furthermore, water abstraction can especially affect the functioning of arid and semi-arid rivers. In particular, interception and assimilation of inorganic nutrients can be detrimental under hydrologically abnormal conditions. Among other effects, abstraction and increased nutrient loading might cause a shift from heterotrophy to autotrophy, through direct effects on primary producers and indirect effects through food webs, even in low-light river systems. The simultaneous desires to conserve and to provide ecosystem services present several challenges, both in research and management.

The value of specially designated sites in conserving biodiversity has been a hotly debated issue for many years in the UK and elsewhere. The debate recently has been given fresh impetus in England by the creation of Natural England, the new Government Agency responsible for the protection and enhancement of the natural environment, and the challenges facing the management of designated sites resulting from the increasingly tangible effects of climate change. In the freshwater environment, the role of designated sites is under a particular spotlight because of the implementation of the European ‘Water Framework Directive’, which aspires to holistic, ecologically based management of aquatic habitats.

This paper explores the underlying premises of, and rationale for, special site designations for wildlife and provides a frank account of the inevitable clash of management philosophies that designations create in the freshwater environment. It draws on experiences of managing designated freshwater sites in England over the past decade from within English Nature, the former statutory agency for nature conservation (succeeded by Natural England). The issues and principles discussed, are however, highly relevant to the rest of the UK, other European Member States and countries further afield.

A positive role is outlined for designated sites in freshwater conservation, which addresses these management conflicts in a way that not only meets Government obligations towards these sites but also paves the way for informed, progressive management of the wider freshwater resource. As part of this account, attempts are made to clarify the relationship between key biodiversity-related policy drivers in the freshwater environment and to explain how the spectre of climate change can be addressed within designated site management. The importance of strategic freshwater science, collaboratively designed and funded, in maximising the value of the designated freshwater site network to the wider freshwater habitat resource, is stressed.

Bacteria are among the most abundant groups of organisms. They mediate key ecological processes. Recent molecular advances have provided greater insight into bacterial diversity as well as allowing a more thorough examination of patterns in the spatial and temporal distribution of bacteria. Thus, the study of bacterial biodiversity and biogeographical distribution has stimulated considerable interest and dispute over the last decade.

This review summarises the findings obtained from studies on the biogeography of bacterioplankton in inland waters. We examine factors and processes that may determine and maintain bacterial diversity and biogeography, and relate these to the theoretical metacommunity framework.

We conclude that the importance of local environmental factors (such as lake character) for local bacterioplankton community compositions (BCC) is much more intensively studied than the importance of regional factors, such as dispersal. Further, few attempts have been made to evaluate simultaneously the relative importance of the two types of factors for BCC. Finally, we summarise gaps in knowledge, delineate challenges and put forward possible future research directions.