This essay introduces the special issue of this journal on the ecology of soil protists. This issue marks approximately the first 100 years of soil protistology as a discipline as some of the first studies to show that protozoa were an important part of soil ecology took place at Rothamsted, in southern England, towards the end of the first decade of the twentieth century. Much of the work on soil protists – and indeed the papers in this special issue – concentrate on traditional protozoa. In addition it is now realised that slime molds (Eumycetozoans) can potentially make an important contribution to the numbers and diversity of soil amoebae. We also argue that diatoms and other algae are likely important in soils and in need of more detailed study. By its nature microbiology (including soil protist ecology) is a science limited by technology – for example the subject could not really exist before the invention of the microscope. We suggest ways in which newer technologies (molecular methods, stable isotopes etc) may contribute to future studies on the ecology of soil protists.

Eumycetozoans, commonly referred to as slime moulds, are common to abundant organisms in soils. Three groups of slime moulds (myxogastrids, dictyostelids and protostelids) are recognized, and the first two of these are among the most important bacterivores in the soil microhabitat. The purpose of this paper is first to provide a brief description of all three groups and then to review what is known about their distribution and ecology in soils.

Current research is reviewed on aquatic and soil microbial ecology with attention to the fate of organic carbon in bacterial-based protist food webs, including some new data. Particular attention is given to the effects of pulsed sources of low-molecular weight organic sources of carbon on soil respiration, changes in bacterial, nanoflagellate, and naked amoeba C-biomass, and evidence for throughput of carbon in microbial food webs in Arctic and some low-latitude, temperate soil environments. The proportion of pulsed sources of glucose-C that is sequestered in microbial biomass relative to loss as CO2 is examined in laboratory experimental studies, and implications of the research for microbial community dynamics and global warming due to terrestrial sources of respiratory CO2 are discussed.

Bacteria, protozoa and nematodes interact closely in soil ecosystems. Protozoa and nematodes eat bacteria (and occasionally each other), while bacteria defend themselves using chemical substances, resistant cell walls, irregular shapes and motility. Protozoa and nematodes are very different types of organisms, and hence apply very different feeding mechanisms; thus many protozoa can pick and choose individual bacterial cells, whereas nematodes ingest bacterial patches more uncritically. Protozoa and nematode are both aquatic organisms whose activity depends on available soil water, but differences in size, motility, resting stages and reproductive strategies mean that the soil physico-chemical environment influences the activity of protozoa and nematodes differently. For example, the relative importance of protozoa compared to nematodes may shift towards protozoa in very clay-rich soils. The interactions between the three organism groups have major ecological consequences such as modification of the bacterial communities and increased nitrogen mineralisation, both of which affect plant growth. Increased nitrogen mineralisation will usually be beneficial for plant growth, whereas the grazing induced changes in the bacterial communities can be both beneficial and detrimental to plants. Selective protozoan grazing can favour plant inhibiting bacteria. This may be a problem in clay rich soils where protozoa have better life conditions than nematodes.

By feeding on bacterial biomass protozoa play an acknowledged role in the liberation of nutrients in the plant rhizosphere. In addition there are suggestions that plants have mechanisms working through changes in root architecture and initiation of active release from soil organic matter, which are used to improve uptake and recirculation of nutrients in the ecosystem. All processes are carried out on a local scale in soil with roots, bacteria and protozoa interacting. The many actors and the small scale of interactions make experimentation difficult. We discuss mistakes, pit falls and misinterpretations and provide suggestions for improvement. Recent methodological progress has opened new exciting avenues for protozoan research. New techniques have already helped to reveal protozoan regulation of cooperation as well as conflict in bacterial communities. These mechanisms in turn affect bacterial functioning and target molecular control points in rhizosphere food webs in relation to plants. Integrating nutritional and regulatory aspects into new concepts of protozoan functioning in soil is a challenging frontier in protozoology.

Bacteria producing secondary metabolites with antagonistic effects on fungal pathogens have received attention during the last decades as an alternative to chemical pesticides. They, however, might also have effects on indigenous soil organisms like bacteria and protozoa, the latter ones being among the most important grazers of bacteria in soil. The present study reports on the effect of the potential biocontrol agent Pseudomonas fluorescens CHA0 and its genetically modified derivative CHA0/pME3424 on indigenous soil bacteria and protozoa in a soil system. CHA0/pME3424 overproduces two of the secondary metabolites produced by CHA0: the polyketide antibiotics pyoluteorin (Plt) and 2,4-diacetylphloroglucinol (DAPG). P. fluorescens CHA0/gfp1 and CHA0/pME3424 both negatively affected the abundance of soil bacteria and protozoa and the genetic community structure of Kinetoplastida studied by PCR-DGGE. The negative effects were detectable after 14 days but were decreasing and are expected to be temporary. The overproducer of secondary metabolites did not differ in effect from the wild type. The soil respiration and bacterial genetic community structure were not significantly affected. The study shows the soil bacteria and protozoa to be temporary affected by bacteria producing secondary metabolites, which can have implications for nutrient-cycling in soil and environmental risks of biocontrol agents.

Testate amoebae (TA) are an important part of soil microbial communities and in certain ecosystems they may represent a substantial proportion of total microbial biomass. Their distribution and abundance is driven by various abiotic factors (e.g. pH, organic matter, soil moisture, soil/water chemistry) but comparatively less is known about the role of biotic interactions. TA often co-occur with Ericaceae, a ubiquitous plant family inhabiting acidic soils with poor nutrient status. Ericaceae can significantly change soil properties through production of recalcitrant litter and possibly also due to root exudates and activities of root-inhabiting fungi; this may result in profound modifications of microbial communities. A recent study from northwest England shows that the invasive ericaceous shrub Rhododendron ponticum may significantly modify communities of soil TA. Here, we investigate the effect of pH, organic matter, soil moisture and R. ponticum presence on TA communities within the native range of the ericaceous shrub at two sites in south Spain and compare our results with the previous study from NW England. At the Spanish sites, organic matter content, R. ponticum presence and pH affected occurrence and abundance of several TA species; R. ponticum presence and organic matter content were highly correlated and explained most of the observed variability in TA communities (= the effect of the R. ponticum rhizosphere). R. ponticum rhizosphere affected especially TA with relatively large tests, i.e. Cyclopyxis eurystoma, Phryganella acropodia and Trigonopyxis arcula. Interestingly, T. arcula was also positively associated with R. ponticum in the previously studied British sites. The rhizosphere of the ericaceous shrub appears to have a positive effect on testate amoebae taxon richness at the two studied autochthonous Spanish sites but may reduce taxon richness in the sites in Britain where R. ponticum is an introduced species. Such possible positive/negative effects of native/invasive species, as well as other plant guilds, on TA communities clearly deserve further investigation.

Few studies have examined testate amoebae assemblages of estuarine tidal marshes. This study investigates the possibility of using soil testate amoebae assemblages of a brackish tidal marsh (Scheldt estuary, Belgium) as a proxy for water level changes. On the marsh surface an elevation gradient is sampled to be analyzed for testate amoebae assemblages and sediment characteristics. Further, vegetation, flooding frequency and soil conductivity have been taken into account to explain the testate amoebae species variation. The data reveal that testate amoebae are not able to establish assemblages at the brackish tidal marsh part with flooding frequencies equal to or higher than 36.5%. Further, two separate testate amoebae zones are distinguished based on cluster analysis. The lower zone’s testate amoebae species composition is influenced by the flooding frequency (~ elevation) and particle size, while the species variability in the higher zone is related to the organic content of the soil and particle size. These observations suggest that the ecological meaning of elevation shifts over its range on the brackish tidal marsh Testate amoeba assemblages in such a brackish habitat show thus a vertical zonation (RMSEP: 0.19 m) that is comparable to the vertical zonation of testate amoebae and other protists on freshwater tidal marshes and salt marshes.