To introduce the special issue this paper reviews the use of protists as bioindicators. Seven key advantages of protist bioindicators are highlighted, namely: environmental sensitivity, functional importance, distribution, size and numbers, response times, ease of analysis and preservation potential. Protist bioindicators have been used in a wide range of contexts from ecosystem restoration to fire history, and particularly environmental pollution. Most major protist groups have been used as bioindicators with diatoms, foraminifera and testate amoebae particularly widely studied. To increase uptake of protist bioindication techniques in routine environmental monitoring technique development should consider the needs of stakeholders from an early stage. Papers in this special issue reflect the diversity of both protist life and possible bioindicator applications.

Proxy based sea-level reconstructions are an important tool for defining past patterns of sea-level change and salt-marsh testate amoebae are a newly emerging proxy with high potential as sea-level indicators. This study develops existing analytical techniques concerned with the preparation and counting of testate amoebae for sea-level studies and demonstrates the predictive power of this group of micro-organisms. Two salt marshes in northwestern Norway were sampled for testate amoebae and multiple sub-samples were prepared using different procedures and count totals. Analytical efficiency can be improved upon by using a mild alkali, chemical disaggregant (5% KOH) to break up fibrous, salt-marsh peat and concentrate tests prior to counting. A count total of 100 individuals, rather than 150, can be used to make time gains with little or no loss of taxon information. The Norwegian salt-marsh testate amoebae showed strong zonation relative to tidal elevation. Key indicator taxa from the high marsh included Centropyxis cassis type, Cyclopyxis arcelloides type and Euglypha spp. Those from the low marsh included Difflugia pristis type and a distinctive morphotype of Centropyxis platystoma type. Combined, the two surface data sets from Norway were capable of predicting marsh surface elevations to within ± 0.09 m.

The nature conservation, and wider environmental importance of peatlands, particularly in relation to carbon management, has led to there being a growing interest in attempting to manage degraded peatlands in a way that will restore them to fully functioning peatland ecosystems. Much of this management is concerned with the rewetting of these sites therefore it has become important to monitor the surface wetness of these bogs and if possible compare current wetness with previous, pre-damage, conditions. We present previously unpublished case studies of the use of testate amoebae to monitor bog restoration schemes in N.W. England (Holcroft Moss, Cheshire) and Ireland (Ardagullion Bog, Co. Longford). In addition we summarise the key conservation related conclusions of our previously published work on two other sites in N.W England – Astley Moss (in the Chat Moss complex of Greater Manchester) and Danes Moss (Cheshire). At Holcroft the record of lead pollution from the peat core allows us to date recent changes in the testate community preserved in a peat core and relate these to both conservation management and other changes in the landscape around the bog in over the last 50 years. Ardagullion Bog provides an illustration of the utility of using multiple peat cores in the testate monitoring of peat bog restoration and illustrates that a bog that has only suffered limited ‘damage’ is able to be restored to something close to pre damage conditions on a decadal time scale. We also summarise what we see as the main lessons from testate studies of bog restoration – both from the case studies described in this paper and from the wider literature - and discuss the conditions under which testate amoebae may be of particular use in peatland restoration.

The benthic foraminiferal assemblages in Lake Varano (southern Italy) have been investigated in detail. Statistical analyses enable us to recognize two main biotopes and five sub-biotopes that reflect different ecological and environmental conditions. The assemblages mainly seem to be influenced by the hydrological (namely salinity) and sediment conditions in the lake. These biotopes are characterized by specific sub-assemblages and variations in relative species’ abundances. The Outer Lake Biotope is affected by marine influence and is dominated by the foraminiferal species Ammonia beccarii, Ammonia parkinsoniana and Aubignyna perlucida, which are more common in open water environments. In contrast, the Inner-Marginal Lake Biotope reflects more restricted conditions where low salinity values and sand are associated with high numbers of miliolids. These two main biotopes are thus subjected to different degrees of confinement and water residence times, both of which are related to the water exchange time of the lake with the Adriatic Sea. In addition five sub-biotopes (Intermediate Marine, Mixing, “Urban”, Marginal, and Innermost) represented by particular foraminiferal assemblages are identified that characterize particular sub-environments. These sub-biotopes are, to some extent, separated by salinity gradients as well as the grain-size and the organic matter of sediments.

Benthic and planktic foraminiferal assemblages from two sediment cores (2000 m depth, 44°33′N-2°45′W) were analyzed to first compare modern and dead faunas and next to study changes in the hydrology of the southeastern Bay of Biscay (SE BoB) over the last 12.8 cal ka BP. Considering benthic ecosystem characteristics, the first part of the paleorecord (12.8–7.6 cal ka BP) is composed of laminated sediments that may have resulted from turbiditic overflow events, whereas occurrences of transported species (e.g. Nonionella sp., Cassidulina carinata) attest of continental influence at the core location. After 7.6 cal ka BP, the sediment becomes bioturbated concomitantly to the stabilization of the sea-level. The benthic foraminiferal fauna is largely dominated by Uvigerina peregrina suggesting a high seasonality with seasonal pulsed organic matter fluxes to the seafloor. On the other hand, the planktic foraminiferal composition indicates that surface water masses were under the influence of the polar front in the early record, which retreated at about 11.5 cal ka BP. The early Holocene is characterized by relatively warm and stratified water masses at 8.4–4.8 cal ka BP. The last 4.8 cal ka BP records a gradual sea surface water cooling trend and enhanced foraminiferal production from ~2.6 cal ka BP until present. The early (12.8–10.5 cal ka BP) and late (2.3–1.7 cal ka BP) Holocene are characterized by the presence of the planktic species Globigerinoides ruber probably caused by intrusions of the Iberian Poleward Current (IPC), and a negative state of the North Atlantic Oscillation (NAO).

Monothalamous foraminifera with organic and agglutinated test walls (‘‘allogromiids’’ sensu lato) deserve attention because of their importance in deep-sea and shallow-water soft-bottom communities and their crucial phylogenetic position at the base of the foraminiferal evolutionary tree. However, our knowledge of the biodiversity and ecology of monothalamous foraminifera is very incomplete and geographically patchy. Here, we present a short review based on the available data on monothalamous, soft-walled foraminiferal taxa from the Adriatic Sea in response to several environmental parameters (i.e., organic matter, oxygen, grain size, depth). The main results of the studies provide evidence of the importance of these foraminiferal taxa in this shallow, temperate latitude area;they represent a start for the identification of soft-shelled monothalamous morphotypes that could be potential bioindicators of environments influenced by inputs of fresh waters, increasing eutrophication and consequent fluctuations in bottom-water oxygenation. The contribution of this soft-shelled component to living benthic foraminiferal assemblages appears not negligible and excluding it from foraminiferal studies can potentially lead to a loss of ecological information. The study, therefore, provide an atlas of the Adriatic soft-shelled foraminiferal taxa in order to 1) encourage the species-level description, if possible, or alternatively a basic morphotype characterization, 2) facilitate future comparisons of taxa from similar settings, 3) promote their potential use in future biomonitoring investigations together with the hard-shelled foraminifera.

Miliolid (calcareous imperforated test) foraminifera have large diffusion all over the world in a wide range of marine environments, but their distributional pattern in relation to heavy metal pollution is not clearly understood yet. The aim of this study was to better understand the biological response of the miliolid species Pseudotriloculina rotunda to experimental chronic exposure at several zinc concentrations. The duration of the experiment was 10 weeks, and six different concentrations of zinc were tested between 0 and 100 mg/L. Increasing zinc concentrations led to increasing delay or to complete cease of the new chambers’ construction, with consequences on growth rates and affected vitality and biomass variations at medium to high concentrations. Moreover, our results showed that, even at high concentrations, zinc did not cause macroscopic test deformities due to anomalous arrangements of chambers.

A survey of the summer phytoplankton communities of thirty-six moderately-deep north temperate lowland lakes showed that the proportions of Dinophyta and non-heterocyst-bearing cyanobacteria taxa, measured as biovolume, were inversely related to the total nitrogen: total phosphorus (TN:TP) ratio and that these groups were predominant in lakes where available nitrogen fell to undetectable concentrations. The proportion of heterocyst-bearing cyanobacteria was positively correlated to the TN:TP ratio and nitrate. Dinophyta and/or non-heterocystous cyanobacteria were prevalent in lakes with the highest epilimnion nutrient concentrations, whilst heterocystous cyanobacteria predominated in lakes with moderate nutrient concentrations. It is argued that the ability of Dinophyta to migrate vertically and to supplement their nutrient requirements though heterotrophy may enable them to be at least as successful as Cyanobacteria in high nutrient lakes and in overcoming nitrogen-scarcity. Our findings provide evidence that Dinophyta can be used as indicators of water quality.