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The shells of testate amoebae are morphologically diverse and persistent in the environment. Accordingly, the examination of the morphology and composition of shells became a standard tool in ecological, palaeoecological, and evolutionary studies. However, so far the function of the shell remains poorly understood and, although based on limited evidence, the shell was considered as a defense mechanism. Based on recent evidence, we propose that the shell of arcellinid testate amoebae is a crucial component facilitating the amoebae's attack of large prey. Accordingly, the shell is not purely protective, but must be considered also as a weapon. This change in perspective opens up numerous new avenues in protistology and will lead to a substantial change in ecological, palaeoecological, and evolutionary research. [ABSTRACT FROM AUTHOR]

Abstract Methodological advances are essential for robust ecological research. Quantitative reconstructions of environmental conditions using testate amoebae rely on sound taxonomy. While the taxonomy of large species is relatively well resolved, this is not the case for most small taxa (typically <45 μm long). In New Zealand, peatlands contain a diversity of both cosmopolitan and characteristic large southern endemic taxa, but also have a high abundance of small taxa. The latter are often lumped into morphotypes reducing their value as ecological indicators. In this study, we demonstrate how (a) lumping small taxa versus splitting them into unique types, and (b) including or excluding them from community analysis influenced their ecological inference. We assessed testate amoeba composition in six peat bogs from New Zealand, three that were moderately-to-highly impacted, and three that were non-impacted. Environmental variables were measured at each sampling site and the surface testate amoeba community patterns and community-environment relationships compared. We found a clear division between impacted and non-impacted sites. Several distinct small taxa were more strongly related to water-table depth and conductivity, while the larger taxa were more correlated to pH. These results show that improved taxonomic resolution of small taxa can provide more informed environmental assessment. [ABSTRACT FROM AUTHOR]

Elevation gradients have been useful to study distributional patterns of soil organisms since the time of Humboldt but only recently these patterns have been studied for soil microorganisms. Here we report the results on species diversity and composition of soil- and moss-dwelling testate amoeba assemblages along a 1400 m elevation gradient (904–2377 m a.s.l.) on Mount Fuji (Japan) from temperate forest to alpine vegetation. In total, 95 testate amoeba taxa belonging to 29 genera were identified. The core of testate amoeba assemblages was formed by ubiquitous species such as Trinema lineare , Euglypha laevis , Cryptodifflugia oviformis , and Trinema complanatum. However, several taxa with limited geographic distribution were also observed (e.g., Centropyxis latideflandriana , C. stenodeflandriana , Plagiopyxis cf. barrosi , Heleopera rectangularis , and Distomatopyxis couillardi). Species diversity indices (species richness and Shannon's index) were characterised by bell-shaped patterns peaking at ∼ 1700 m in the subalpine mixed conifer-deciduous forest. The species composition of testate amoeba assemblages was best explained by the vegetation types which accounted for 12.3% of the total variation. Overall, these findings indicate that elevation effects on species composition of testate amoeba assemblages are strongly mediated by vegetation. [ABSTRACT FROM AUTHOR]

Abstract: Peatland testate amoebae are widely used to reconstruct paleohydrological/climatic changes, but many species are also known to respond to pollutants. Peatlands around the world have been exposed to anthropogenic and intermittent natural pollution through the late Holocene. This raises the question: can pollution lead to changes in the testate amoeba paleoecological record that could be erroneously interpreted as a climatic change? To address this issue we applied testate amoeba transfer functions to the results of experiments adding pollutants (N, P, S, Pb, O3) to peatlands and similar ecosystems. We found a significant effect in only one case, an experiment in which N and P were added, suggesting that pollution-induced biases are limited. However, we caution researchers to be aware of this possibility when interpreting paleoecological records. Studies characterising the paleoecological response to pollution allow pollution impacts to be tracked and distinguished from climate change. [Copyright &y& Elsevier]

A massive tufa complex in the lower Lorze Valley (550 m a.s.l., north-central Switzerland) formed between 9000 and 5000 cal. yr BP. In the plain 4 km southeast of the complex lies Neugrundmoor (830 m a.s.l.), a mire in the hydrologic recharge area of the springs responsible for the tufa formation. Here we address an earlier, untested hypothesis that the transition of Neugrundmoor from fen to raised bog caused the end of the tufa formation, by means of pollen and testate amoebae analyses on a peat section. The chronology of the section is based on ten AMS 14C-dates of terrestrial plant macrofossils. Our results suggest that until 7100 cal. yr BP the plain had shallow ponds, which gradually developed into fens. Starting 5350 cal. yr BP, large raised bogs developed in the fens in a few centuries. This agrees with the hypothesis that the end of tufa formation coincided with the transition from fen to raised bog. It also coincided with the end of the mid-Holocene temperature optimum, when climate became cooler and wetter. We suggest that the main factor causing the end of tufa formation at 5500-5000 cal. yr BP was declining air temperatures, which on the one hand led to diminished calcium precipitation, on the other to enhanced bog formation. Peat has a low hydraulic conductivity, so we suggest that less water became available for tufa formation because of increased thickness of peat layers, exacerbating the direct effect of cooling on calcium precipitation. Noticeable human influence in the surroundings did presumably not start before c. 3500 cal. yr BP and was then very weak, so this was not responsible for the end of the tufa formation. Extrapolation of our results suggests that climatic cooling alone is sufficient to explain the widespread termination of tufa formation after the mid Holocene. [ABSTRACT FROM AUTHOR]

New Zealand (NZ) is a well-known hotspot of biodiversity and endemism for macroscopic organisms, but its microbial diversity is comparatively poorly documented. We assembled all records on NZ testate amoebae published since the early 20th century and present a comprehensive taxonomic checklist for NZ. Testate amoebae are reported from six major habitat types across both the North and South Islands of NZ, but the sampling effort is ecologically and geographically biased in favour of wetlands and the South Island. As a result, 93% of all 128 morphotypes recorded in NZ occur in wetlands, 28% are restricted to the South Island, and diversity is greater at higher latitudes. Around 50% of morphotypes have a broad latitudinal distribution across the NZ mainland, whereas 15% have narrow latitudinal ranges. Future research should aim to broaden the geographical and ecological ranges. We predict that our list of NZ testate amoebae will expand substantially with future work, and that the latitudinal diversity gradient will be inverted. We also introduce an interactive, fully illustrated, online Lucid key for the rapid identification of NZ testate amoebae. As many morphospecies are cosmopolitan, this key provides a useful tool for testate amoebae identification in other parts of the world. [ABSTRACT FROM AUTHOR]

To date only five partial and two complete SSU rRNA gene sequences are available for the lobose testate amoebae (Arcellinida). Consequently, the phylogenetic relationships among taxa and the definition of species are still largely dependant on morphological characters of uncertain value, which causes confusion in the phylogeny, taxonomy and the debate on cosmopolitanism of free-living protists. Here we present a SSU rRNA-based phylogeny of the Hyalospheniidae including the most common species. Similar to the filose testate amoebae of the order Euglyphida the most basal clades have a terminal aperture; the ventral position of the pseudostome appears to be a derived character. Family Hyalospheniidae appears paraphyletic and is separated into three clades: (1) Heleopera sphagni, (2) Heleopera rosea and Argynnia dentistoma and (3) the rest of the species from genera Apodera, Hyalosphenia, Porosia and Nebela. Our data support the validity of morphological characters used to define species among the Hyalospheniidae and even suggest that taxa described as varieties may deserve the rank of species (e.g. N. penardiana var. minor). Finally our results suggest that the genera Hyalosphenia and Nebela are paraphyletic, and that Porosia bigibbosa branches inside the main Nebela clade. [Copyright &y& Elsevier]

Testate amoebae are useful environmental indicators in ecological and palaeoecological studies from peatlands. Previous quantitative studies have focused on the peatlands of Northern and Central Europe, North America, and New Zealand and have considered a relatively restricted variety of peatland types, mostly ombrotrophic or Sphagnum-dominated while more minerotrophic fens have been less studied. Here we present the first quantitative ecological study of testate amoebae from four small mesotrophic fens (pH 5.5–8.1) in the Elatia Forest, northern Macedonia province, Greece. Relationships with the environmental data were investigated using redundancy analysis and mantel tests. Transfer function models were derived using a variety of techniques. Results demonstrate that as for Sphagnum-dominated mires hydrology is the most important control on amoebae community composition. Transfer function models should enable water tables to be predicted within 2.5cm, when data selection is used this is reduced to less than 2cm. pH is also an important environmental control on testate amoebae communities, a transfer function model enables pH prediction within 0.4 pH units. The hydrological transfer function is the best performing such model yet produced in terms of prediction error. This study provides new data on the ecology of testate amoebae in fens, and the transfer function models should allow quantitative palaeohydrological reconstruction. [Copyright &y& Elsevier]

Testate amoebae are a diverse group of shelled protists frequently used as model organisms in microbial biogeography. Relatively few species have been reported for the Southern Hemisphere, however, it remains unclear whether this lower diversity is real or an artifact of under-sampling or misidentifications, which would reduce their potential to address macroecological questions. We evaluated testate amoebae diversity from the full range of habitats occurring within two Tierra del Fuego peatlands and compared it with the reported diversity for the area and from the Northern Hemisphere peatlands. We recorded 87 species, of which 69 are new for the region and 45 of them probably new to science and likely to have restricted geographical distributions. Combined with previous studies, the total diversity of testate amoebae only from Tierra del Fuego peatlands now reaches 119, as compared with 183 reported from all Northern Hemisphere peatlands. Our results demonstrate that the number of Gondwanian and Neotropical endemic testate amoeba may be substantially higher than currently known. Previous reports of Holarctic taxa in Tierra del Fuego may result from forcing the identification of morphotypes to the descriptions in the most common literature (force-fitting) South American species into species common in literature from other regions. [ABSTRACT FROM AUTHOR]

Testate amoebae are a widely-used tool for palaeohydrological reconstruction from peatlands. However, it has been observed that weak idiosomic siliceous tests (WISTs) are common in uppermost peats, but very rarely found as subfossils deeper in the peat profile. This taphonomic problem has been noted widely and it has been established that WISTs disaggregate and/or dissolve in the low pH condition of ombrotrophic peatlands. Here we investigate the effect of this taphonomic problem on water-table reconstructions from thirty European peatlands through the comparison of reconstructions based on all taxa and those with WISTs removed. In almost all cases the decomposition of WISTs does not introduce discernible bias to peatland water-table reconstructions. However, some discrepancy is apparent when large abundances of Corythion-Trinema type are present (9−12 cm deviation with 50–60% abundance of this particular taxon). We recommend that WISTs should be removed before carrying out water-table reconstructions, and that the minimum count of testate amoebae per sample should exclude WISTs to ensure the development of robust reconstructions. [ABSTRACT FROM AUTHOR]

Monitoring tools are needed to assess changes in peatland biotic communities and ecosystem functions in response to on-going climate and other environmental changes. Although the responses of soil organisms and plants to ecological gradients and perturbations do not always correlate, peatland monitoring is mainly based on vegetation surveys. Testate amoebae, a group of protists, are important contributors to carbon and nitrogen cycling in organic soils and are useful bioindicators in peatland ecology and paleoecology. There is however little comparative data on the value of testate amoebae, vascular plants and bryophytes as bioindicators of micro-environmental gradients in peatlands. We compared the relationships of testate amoebae, bryophytes, and vascular plants with soil temperature, water table depth, micro-habitats and the carbon and nitrogen content of Sphagnum mosses in four peatlands along a 1300 m altitudinal gradient in Switzerland. We used the full diversity of vascular plants and bryophyte but only a selection of ten easily identifiable testate amoeba morpho-taxa (i.e. species or species-complexes). Indirect and direct gradient ordinations, multiple factor analysis (MFA) and transfer function models for inferring water table depth showed that a selection of ten testate amoeba taxa are more powerful (% variance explained in RDA) and accurate (discrimination among habitats) indicators of local conditions (micro-habitat type, water table depth and Sphagnum C/N ratio) than the vegetation (vascular plants and bryophytes either individually or combined and considering the full diversity). Our study showed that a limited list of ten easily identifiable testate amoeba taxa have higher bioindication value than the full bryophytes and vascular plants. Furthermore, testate amoebae can be analyzed on samples collected at any season (accessibility allowing and if precise sampling sites are well marked) – a clear advantage for biomonitoring and can be used to infer past changes from the peat record at the same taxonomic resolution. This simple approach could therefore be very useful for biomonitoring of peatlands. [ABSTRACT FROM AUTHOR]

In the last two centuries, a high proportion of peatlands have been lost or severely degraded across the world. The value of peatlands is now well-recognised for biodiversity conservation, flood management, and carbon mitigation, with peatland restoration now central to many government policies for climate action. A challenge, however, is to determine 'natural' and 'disturbed' conditions of peatlands to establish realistic baselines for assessing degradation and setting restoration targets. This requires a tool or set of tools that can rapidly and reliably capture peatland condition across space and time. Our aim was to develop such a tool based on combined analysis of plant and testate amoebae; a group of shelled protists commonly used as indicators of ecological change in peatlands. The value of testate amoebae is well established in Northern Hemisphere Sphagnum -dominated peatlands; however, relatively little work has been undertaken for Southern Hemisphere peat forming systems. Here we provide the first assessment and comparison of the bioindicator value of testate amoebae and vascular plants in the context of Southern Hemisphere peatlands. Our results further demonstrate the unique ecohydrological dynamics at play in New Zealand peat forming systems that set them apart from Northern Hemisphere peatlands. Our results show that plant and testate amoeba communities provided valuable information on peatland condition at different scales, we found that testate amoebae tracked changes in the abiotic variables (depth to water table, pH, and conductivity) more closely than vascular plants. Our results further demonstrate that functional traits of testate amoebae showed promising relationships with disturbance. Amoeba test compression, aperture position and test size were linked to changes in hydrology driven by fluctuations in ground water tables; however, trait responses manifested differently in ombrotrophic and minerotrophic peatlands. Overall, testate amoebae provide a promising bioindicator for tracking degradation in New Zealand peatlands and a potential additional tool to assess peatland condition. • The first assessment and comparison of the bioindicator value of testate amoebae and vascular plants in Southern Hemisphere peatlands. • Testate amoebae are a promising bioindicator for tracking degradation in New Zealand peatlands and are a potential tool for peatland managers. • Testate amoebae tracked changes in the abiotic variables more closely than vascular plants in New Zealand peatlands. • Functional trait analysis of testate amoebae enriches our understanding of microorganism response to degradation in peatlands. [ABSTRACT FROM AUTHOR]

In the decade since the first pan-European testate amoeba-based transfer function for peatland palaeohydrological reconstruction was published, a vast amount of additional data collection has been undertaken by the research community. Here, we expand the pan-European dataset from 128 to 1799 samples, spanning 35° of latitude and 55° of longitude. After the development of a new taxonomic scheme to permit compilation of data from a wide range of contributors and the removal of samples with high pH values, we developed ecological transfer functions using a range of model types and a dataset of ∼1300 samples. We rigorously tested the efficacy of these models using both statistical validation and independent test sets with associated instrumental data. Model performance measured by statistical indicators was comparable to other published models. Comparison to test sets showed that taxonomic resolution did not impair model performance and that the new pan-European model can therefore be used as an effective tool for palaeohydrological reconstruction. Our results question the efficacy of relying on statistical validation of transfer functions alone and support a multi-faceted approach to the assessment of new models. We substantiated recent advice that model outputs should be standardised and presented as residual values in order to focus interpretation on secure directional shifts, avoiding potentially inaccurate conclusions relating to specific water-table depths. The extent and diversity of the dataset highlighted that, at the taxonomic resolution applied, a majority of taxa had broad geographic distributions, though some morphotypes appeared to have restricted ranges. [ABSTRACT FROM AUTHOR]

Abstract: Among the non-pollen micro-fossils commonly encountered in Quaternary sediment samples prepared for pollen analysis are many shells of testate amoebae. Testate amoebae are eukaryotic micro-organisms which are increasingly used in ecological and palaeoecological studies, particularly as indicators of hydrological change in Sphagnum-dominated peatlands. In this study we address the extent to which testate amoebae are used in palynological research, the key challenges to more widespread use, and the extent to which ecological information is retained in the testate amoeba assemblages of standard palynological slides. To achieve this we review the literature on the use of testate amoebae in palynology, compare testate amoeba records produced by palynological and water-based preparation methods and carry out simulations using previously-derived datasets. Our results show that testate amoebae are widely encountered in Quaternary palynological studies, primarily in peatlands, but the information which they can provide is undermined by limited taxonomic knowledge. Many taxa are destroyed in pollen preparations, but for taxa that are retained patterns of abundance parallel those determined using water-based preparation methods. Although the loss of sensitive taxa limits the ecological information contained in testate amoeba assemblages the information preserved is likely to be useful in a multiproxy approach to palaeoenvironmental reconstruction. To help improve taxonomic awareness and encourage the use of testate amoebae in palynology we present a basic introduction to testate amoeba taxonomy and a guide to the taxonomic literature. [Copyright &y& Elsevier]

Abstract: Functional traits (FT) offer a new framework to understand the ecology of organisms and overcome taxonomic difficulties that currently limit the study of minute soil taxa. FT are likely to be selected by environmental filters and hence they may provide more direct information on ecosystem characteristics than the species composition of a community. We tested the potential of testate amoeba (TA) functional traits as bioindicators of selected ecosystem processes in the context of a restored floodplain in north-western Switzerland. The floodplain was divided into six functional process zones (FPZs) associated to distinct post-restoration successional stages. We selected TA FT and computed three functional indices: functional richness (FRic), divergence (FDiv), evenness (FEve), and dispersion (FDis). We then compared the patterns of functional indices and classical diversity indices such as species richness, diversity and evenness. We assessed whether traits converged or were over-dispersed in the different FPZs using a randomization procedure. Finally, we related environmental variables and functional traits using the “Fourth Corner” statistic. This procedure enabled us to highlight relations that can potentially be used for bioindication. Promising candidates include the relationships between shell biovolume and vegetation structure and between shell compression and plant litter input variables. [Copyright &y& Elsevier]

Testate amoebae (TA) are a common and diverse group of protists and are especially abundant in peatlands. The structure of peatland TA communities is well correlated to surface moisture and water table depth (WTD). For that reason, TA are widely used as proxy indicators in ecological and palaeoecological studies. Peatlands are abundant across Asia, but the diversity and ecology of the TA that inhabit these systems are poorly documented. It is therefore unclear whether TA can be used as palaeohydrological indicators in the manner in which they commonly are in Europe and North-America. There is particular uncertainty as to the efficacy of this approach in the lower latitudes. We compiled existing and new data on testate amoebae from 1124 Sphagnum -dominated samples from 42 individual peatlands covering broad latitudinal (25°–66° N) and longitudinal (68°–129° E) ranges. Using a consensus taxonomic framework, we built a checklist of TA and developed TA-based hydrological transfer functions for Asian peatlands. The results showed that three models, weighted averaging (WA), weighted average partial least squares (WA-PLS), and maximum likelihood (ML), predicted similar WTD values for full samples, while the modern analogue technique (MAT) produced the strongest (R2 boot = 0.58) relationship between observed and estimated water-table depths (WTDs). Removing outlier samples improved the R2 values of observed vs. estimated WTDs, with ML then demonstrating the strongest predictive power (R2 boot = 0.68, RMSEP boot = 8.98 cm). The predictive capability of the developed WTD transfer function is comparable to equivalent models for Europe and North America and thus can be used for palaeohydrological reconstructions for boreal to subtropical peatlands in Asia. • A testate amoebae taxonomic checklist was compiled from Asian peatlands. • We developed continental scale testate amoeba-based hydrological transfer functions. • The water-table depth transfer functions can be used for paleohydrological reconstructions. [ABSTRACT FROM AUTHOR]

Summary Life was microbial for the majority of Earth's history, but as very few microbial lineages leave a fossil record, the Precambrian evolution of life remains shrouded in mystery. Shelled (testate) amoebae stand out as an exception with rich documented diversity in the Neoproterozoic as vase-shaped microfossils (VSMs). While there is general consensus that most of these can be attributed to the Arcellinida lineage in Amoebozoa, it is still unclear whether they can be used as key fossils for interpretation of early eukaryotic evolution. Here, we present a well-resolved phylogenomic reconstruction based on 250 genes, obtained using single-cell transcriptomic techniques from a representative selection of 19 Arcellinid testate amoeba taxa. The robust phylogenetic framework enables deeper interpretations of evolution in this lineage and demanded an updated classification of the group. Additionally, we performed reconstruction of ancestral morphologies, yielding hypothetical ancestors remarkably similar to existing Neoproterozoic VSMs. We demonstrate that major lineages of testate amoebae were already diversified before the Sturtian glaciation (720 mya), supporting the hypothesis that massive eukaryotic diversification took place in the early Neoproterozoic and congruent with the interpretation that VSM are arcellinid testate amoebae. Highlights • Arcellinida testate amoebae are comprised of seven major lineages • Reconstructed hypothetical ancestral states are congruent with Tonian fossils • Combined analysis of phylogenies and fossils suggest divergence as early as 730 mya Arcellinid testate amoebae are some of the earliest eukaryotic microbes. Lahr et al. show that these amoebae have seven major deep phylogenetic lineages, probably diverged as early as 730 mya. Diversification of these microbes in the mid-Neoproterozoic was probably happening alongside the gradual oxygenation of oceans. [ABSTRACT FROM AUTHOR]