Soil Protists Research Articles

Oxytetracycline and Ciprofloxacin Exposure Altered the Composition of Protistan Consumers in an Agricultural Soil.

Protists, an integral component of soil microbiome, are one of the main predators of bacteria. Bacteria can produce toxic secondary metabolites, e.g., antibiotics to fight stress under the predation pressure of protists; however, impacts of antibiotics on the profile of protists in soils remain unclear. Here, we constructed a microcosm incubation to investigate the effects of two common antibiotics, oxytetracycline and ciprofloxacin, on the protistan and bacterial communities in an arable soil. Rhizaria were the most abundant protist supergroup, followed by Amoebozoa, Stramenopiles, and Aveolata. Among trophic functional groups, consumers were predominant within the protistan community. The protistan alpha-diversity was not significantly changed, while the bacterial alpha-diversity was decreased under the pressure of antibiotics. Nevertheless, the antibiotic exposure considerably reduced the relative abundance of protistan lineages in Rhizaria and Amoebozoa, which were the dominant supergroups of protistan consumers, while increased the relative abundance of other consumer and phototrophic protists. Altogether, we provide novel experimental evidence that the bacterivorous consumers, an important functional group of protists, were more sensitive to antibiotics than other functional groups. Our findings have potential implications for the induced alterations of protistan community and their ecological functions under the scenarios of projected increasing global antibiotic usage.

Global radiation in a rare biosphere soil diatom

Soil micro-organisms drive the global carbon and nutrient cycles that underlie essential ecosystem functions. Yet, we are only beginning to grasp the drivers of terrestrial microbial diversity and biogeography, which presents a substantial barrier to understanding community dynamics and ecosystem functioning. This is especially true for soil protists, which despite their functional significance have received comparatively less interest than their bacterial counterparts. Here, we investigate the diversification of Pinnularia borealis, a rare biosphere soil diatom species complex, using a global sampling of >800 strains. We document unprecedented high levels of species-diversity, reflecting a global radiation since the Eocene/Oligocene global cooling. Our analyses suggest diversification was largely driven by colonization of novel geographic areas and subsequent evolution in isolation. These results illuminate our understanding of how protist diversity, biogeographical patterns, and members of the rare biosphere are generated, and suggest allopatric speciation to be a powerful mechanism for diversification of micro-organisms.

Soil protist communities in burrowing and casting hotspots of different earthworm species

Biotic interactions in the soil food web have been increasingly recognized as crucial for ecosystem functioning, however there are still knowledge gaps in terms of the associations between macrofauna and microorganisms, particularly in soil hotspot microsites. A manipulative study was performed to investigate the protist community in the drilosphere and casts of three earthworm species (epigeic Amynthas cortices, anecic Amynthas hupeiensis and endogeic Drawida gisti) and a control soil without earthworms. Results showed that earthworm presence significantly increased the relative abundance of parasitic protists (p < 0.05). The diversity of protists within drilosphere and casts depended on earthworm species, with D. gisti and A. hupeiensis increasing diversity and A. cortices decreasing protist diversity (p < 0.05). Structural equation modelling indicated that protist abundance and diversity in the drilosphere were regulated indirectly via neutralized soil pH and accelerated C and N mineralization, while in casts were affected directly through earthworm gut processing and indirectly through elevated water content. In conclusion, the marked effects on soil protist community mediated by earthworms varied from distinct earthworm species and microsites. The present study suggests the necessity to consider interactions between protist and earthworms in evaluating the effects of soil fauna on soil biota and the related ecosystem processes.

Land use as a driver for protist community structure in soils under agricultural use across Europe

Soil biodiversity is threatened by intensification of land use. The consequences of different land use on belowground biodiversity remain insufficiently explored for soil protists. Alongside being abundant and extremely diverse in soil, protists provide many ecosystem services: key players in the microbial loop, turnover of organic matter and stimulation of plant growth-promoting rhizobacteria. However, we lack knowledge of effects of site, land use intensity and management on diversity of soil protists. Here we assessed protist communities in four European arable sites with contrasting land use intensities at each site: Lusignan, France; Moskanjci, Slovenia; Castro Verde, Portugal and Scheyern, Germany as well as two grassland sites: Hainich, Germany and Lancaster, UK. Each site has consistent agricultural management history of low and high land use intensities quantified in terms of land use index (LUI). We employed high-throughput sequencing of environmental DNA, targeting the V4 region of the 18S rRNA gene. By assigning the protist composition to trophic groups, we inspected for effects of management, and other biotic and abiotic variables. While overall protist richness was unaffected by LUI within sites, specific trophic groups such as plant pathogens and saprotrophs were affected. Effects on protist biome across land uses and sites were also observed. LUI sensitive taxa were taxonomically diverse in each plot, and their trophic groups responded in specific patterns to specific practices. The most abundant trophic group was phagotrophs (73%), followed by photoautotrophs (16%), plant pathogens (4%), animal parasites (2%) and saprotrophs (1%). Community compositions and factors affecting the structure of individual trophic groups differed between land uses and management systems. The agricultural management selected for distinct protist populations as well as specific functional traits, and the protist community and diversity were indeed affected by site, LUI and management, which indicates the ecological significance of protists in the soil food web.

The global-scale distributions of soil protists and their contributions to belowground systems.

Protists are ubiquitous in soil, where they are key contributors to nutrient cycling and energy transfer. However, protists have received far less attention than other components of the soil microbiome. We used amplicon sequencing of soils from 180 locations across six continents to investigate the ecological preferences of protists and their functional contributions to belowground systems. We complemented these analyses with shotgun metagenomic sequencing of 46 soils to validate the identities of the more abundant protist lineages. We found that most soils are dominated by consumers, although parasites and phototrophs are particularly abundant in tropical and arid ecosystems, respectively. The best predictors of protist composition (primarily annual precipitation) are fundamentally distinct from those shaping bacterial and archaeal communities (namely, soil pH). Some protists and bacteria co-occur globally, highlighting the potential importance of these largely undescribed belowground interactions. Together, this study allowed us to identify the most abundant and ubiquitous protists living in soil, with our work providing a cross-ecosystem perspective on the factors structuring soil protist communities and their likely contributions to soil functioning.

Soil protist diversity in the Swiss western Alps is better predicted by topo‐climatic than by edaphic variables

AbstractAimTrends in spatial patterns of diversity in macroscopic organisms can be well predicted from correlative models, using topo‐climatic variables for plants and animals allowing inference over large scales. By contrast, diversity in soil microorganisms is generally considered as mostly driven by edaphic variables and, therefore, difficult to extrapolate on a large spatial scale based on predictive models. Here, we compared the power of topo‐climatic versus edaphic variables for predicting the diversity of various soil protist groups at the regional scale.LocationSwiss western Alps.TaxaFull protist community and nine clades belonging respectively to three functional groups: parasites (Apicomplexa, Peronosporomycetes and Phytomyxea), phagotrophs (Sarcomonadea, Tubulinea and Spirotrichea) and phototrophs (Chlorophyta, Trebouxiophyceae and Diatomeae).MethodsWe extracted soil DNA from 178 sites along a wide range of elevations with a random‐stratified sampling design. We defined protist Operational Taxonomic Units assemblages by metabarcoding of the V4 region of the rRNA small subunit gene. We assessed and modelled the diversity (Shannon index) patterns of all above‐mentioned taxonomic groups based on topo‐climatic (topography, slope southness, slope steepness and average summer temperature) and edaphic (soil temperature, relative humidity, pH, electroconductivity, phosphorus percentage, carbon/nitrogen, loss on ignition and shale percentage) variables in Generalized Additive Models (GAM).ResultsThe respective significance of topo‐climatic and edaphic variables varied among taxonomic and—to a certain extent—functional groups: while many variables explained significantly the diversity of the three phototrophs this was less the case for the three parasites. Topo‐climatic variables had a better predictive power than edaphic variables, yet predictive power varied among taxonomic groups.Main conclusionsTopo‐climatic variables (particularly slope steepness and summer temperature if we consider their significance in the GAMs) were, on average, better predictors of protist diversity at the landscape scale than edaphic variables. However, the predictive power of these variables on diversity differed considerably among taxonomic groups; such relationships may be due to direct and/or indirect (e.g. biotic) influences (like with parasitic taxa, where low predictive power is most likely explained by the absence of information on the hosts’ distribution). Future prospects include using such spatial models to predict hotspots of diversity and disease outbreaks.

Provisional checklist of terrestrial heterotrophic protists from Antarctica

AbstractHeterotrophic soil protists encompass lineages that are both evolutionarily ancient and highly diverse, providing an untapped wealth of scientific insight. Yet the diversity of free-living heterotrophic terrestrial protists is still largely unknown. To contribute to our understanding of this diversity, we present a checklist of heterotrophic protists currently reported from terrestrial Antarctica, for which no comprehensive evaluation currently exists. As a polar continent, Antarctica is especially susceptible to rising temperatures caused by anthropogenic climate change. Establishing a baseline for future conservation efforts of Antarctic protists is therefore important. We performed a literature search and found 236 taxa identified to species and an additional 303 taxa identified to higher taxonomic levels in 54 studies spanning over 100 years of research. Isolated by distance, climate and the circumpolar vortex, Antarctica is the most extreme continent on Earth: it is not unreasonable to think that it may host physiologically and evolutionarily unique species of protists, yet currently most species discovered in Antarctica are considered cosmopolitan. Additional sampling of the more extreme intra-continental zones will probably result in the discovery of more novel and unique taxa.

Influence of forest type on dark-spored myxomycete community in subtropical forest soil, China

Myxomycetes are the most species-rich Amoebozoa group and one of the major components of soil protist diversity. However, information on their ecology in soil remains surprisingly scarce, since most ecological myxomycete studies focused on microhabitats where fruiting bodies occur. Using DNA metabarcoding method, this study investigated the community of dark-spored myxomycetes in the soil of a subtropical forest in central China. The main predictors of their diversity and community structure were determined based on floristic, edaphic, and seasonal factors. A total of 195 operational taxonomic units (OTUs) were detected in 75 soil samples representing six different forest types. Based on sequence similarity, eight myxomycetes were identified, including three nivicolous species that were recorded for the first time in China. The α-diversity and community structure differed significantly between the investigated forest types, and the highest α-diversity was observed in Pinus armandii forests. However, no seasonality was detected for the myxomycete community. Among the investigated environmental factors, forest type was the strongest predictor of the community composition, and soil pH, C:N ratio, and other spatial factors were also significantly correlated with myxomycete communities. In summary, this study provides new insight into the diversity of soil-inhabiting myxomycetes and indicates a strong effect of vegetation on their community composition.

English

Testate amoebae are a group of free-living heterotrophic protists that have an organic shell or test and play a very good role as bioindicators in the ecological monitoring of environment. Inspite of the importance the percentage contribution of free living protozoans recorded from the Himalayan landscape is only about 12% of the total free living protozoans of India. This portrays a meagre diversity of species from such a highly diversified ecosystem of Himalaya and the true diversity may be far above the recorded number of species. In this study it is herewith reporting two species of testate amoebae viz., Assulina quadratum Van Oye, 1958 and Cyclopyxis leidy Couteaux et Chardez, 1981 for the first time from India from Sangla Valley, Himachal Pradesh. &nbsp; Key words: Assulina quadratum, Cyclopyxis leidy, bioindicator protists, moss-dwelling testate amoebae, soil protists, new biogeographic records, Sangla Valley, Himachal Pradesh, India.

Functional Traits and Spatio-Temporal Structure of a Major Group of Soil Protists (Rhizaria: Cercozoa) in a Temperate Grassland.

Soil protists are increasingly appreciated as essential components of soil foodwebs; however, there is a dearth of information on the factors structuring their communities. Here we investigate the importance of different biotic and abiotic factors as key drivers of spatial and seasonal distribution of protistan communities. We conducted an intensive survey of a 10 m2 grassland plot in Germany, focusing on a major group of protists, the Cercozoa. From 177 soil samples, collected from April to November, we obtained 694 Operational Taxonomy Units representing >6 million Illumina reads. All major cercozoan taxonomic and functional groups were present, dominated by the small flagellates of the Glissomonadida. We found evidence of environmental selection structuring the cercozoan communities both spatially and seasonally. Spatial analyses indicated that communities were correlated within a range of 3.5 m. Seasonal variations in the abundance of bacterivores and bacteria, followed by that of omnivores suggested a dynamic prey-predator succession. The most influential edaphic properties were moisture and clay content, which differentially affected each functional group. Our study is based on an intense sampling of protists at a small scale, thus providing a detailed description of the biodiversity of different taxa/functional groups and the ecological processes involved in shaping their distribution.

Microbial amendments alter protist communities within the soil microbiome

Plant-beneficial microbes improve while pathogens reduce plant performance. When introduced in soils, such microbes can induce entire microbiome changes. However, the impact of those microbial introductions on protists – key predators within the soil microbiome – remain unknown. Here, we tracked how soil protists respond to bacterial (Bacillus and Ralstonia) and fungal (Trichoderma and Fusarium) introductions, with both microbial groups represented by one beneficial and one pathogenic taxon. We found that plant-beneficial Bacillus bacteria change the protist community structure. This community-shift was likely induced by an increased fungi/bacteria ratio, supported by a negative correlation of the fungi/bacteria ratio with the relative abundance of phagotrophic protists across all treatments. Our results indicate that microbial introductions can impact protist communities, thereby altering microbiome-derived multi-functionality.

Soil Testate Amoebae and Diatoms as Bioindicators of an Old Heavy Metal Contaminated Floodplain in Japan.

Soil protists are rarely included in ecotoxicological investigations, despite their fundamental role in ecological processes. Moreover, testate amoebae and diatoms contribute considerably to silicon fluxes in soils. We investigated the effects of heavy metals on testate amoebae (species and individual densities) and diatoms (individual densities) in aged soils of a floodplain (Watarase retarding basin, Japan) taking soil samples from two unpolluted reference sites and two polluted sites. The total concentrations of Cu, Pb, and Zn in soil were higher at the polluted sites as compared with the reference sites. The available concentrations of Co, Cu, and Zn in CaCl2 extracts were higher at the polluted sites but available Pb was not detectable. Testate amoeba taxonomic richness was higher in the reference sites (45/38 taxa) than in the polluted sites (36/27 taxa). The reference sites had higher diatom and amoeba densities than the polluted sites. There was a significant negative correlation between total testate amoeba density and heavy metal concentration (available Co), while significant negative correlations were found between diatom density and Co, Cu, and Zn (available and total concentration). Densities of Cyclopyxis kahli cyclostoma, Centropyxis spp., and Trinema complanatum were negatively correlated to concentrations of available heavy metals. The observed decrease in individual numbers due to heavy metal pollution resulted in a considerable decline in protozoic (testate amoebae) and protophytic (pennate diatoms) silicon pools. Our data suggest that heavy metal pollution affects biogeochemical cycling in this system.

The Past, Present and Future of Soil Protist Ecology Introduction to special issue

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.

Earthworms modulate the effects of climate warming on the taxon richness of soil meso- and macrofauna in an agricultural system

Anthropogenic climate change is altering the functioning of terrestrial ecosystems. Agricultural systems are particularly vulnerable to climate change as they are frequently disturbed by intensified management practices. This also threatens belowground organisms that are responsible for providing crucial ecosystem functions and services, such as nutrient cycling and plant disease suppression. Amongst these organisms, earthworms are of particular importance as they can modulate the effects of climate change on soil organisms by modifying the biotic and abiotic soil conditions. However, they are also known to decline under intensified management, justifying their use as key biotic indicators of intensified agriculture. Yet, our knowledge of the responses of belowground species to the interacting effects of warming and land-use intensification (simulated by earthworm reduction in the experimental setup) remains limited. Here, we tested the interactive effects of soil warming and reduced earthworm densities on soil protists, nematodes, meso- and macrofauna, and their diversity in a common barley system in the Hohenheim Climate Change Experiment. We found that belowground species richness was lowest at elevated temperature and reduced earthworm densities, indicating that earthworms can buffer warming effects on belowground biodiversity. Furthermore, warming increased the densities of plant-feeding nematodes, and herbivorous macrofauna benefitted from reduced earthworm densities. Our results indicate that warming and reduced earthworm densities may simultaneously modify the functioning and service provisioning of soils via shifts in diversity and density of soil biota that would likely lead to simplified belowground food webs. These findings thus highlight the importance of maintaining greater densities of ecosystem engineers like earthworms that may help buffering the detrimental effects of climate warming in agricultural systems.

Food Choice Experiments Indicate Selective Fungivorous Predation in Fisculla terrestris (Thecofilosea, Cercozoa)

Thecofilosea is a class in Cercozoa comprising mainly freshwater inhabiting algivores. Since direct observation of amoeboid protists in soil is not possible, the prey spectra of their terrestrial relatives remain obscure. To test for grazing selectivity and the preferred prey of terrestrial thecofiloseans, we conducted a food choice experiment including yeasts and algae as prey. When being offered all food sources at once, the yeast cells were strongly reduced, whereas the abundance of the algae only slightly decreased. Since Fisculla terrestris thrives with fungal prey, it must be considered as a predator of eukaryotes with high preference for fungal cells.

Toxicity of cadmium and zinc to small soil protists

Small heterotrophic protists (flagellates and naked amoebae) are very abundant in soil and play a key role in maintaining soil services. Hence, knowledge on how xenobiotics affect these organisms is essential in ecosystem management. Cadmium (Cd) is an increasing environmental issue as both industrial deposition and recycling of heavy metal rich waste products have led to Cd enrichment of soils. Evaluation of toxicity of Cd to micro-organisms is often performed using a solution of pure Cd (e.g. CdCl) in liquid culture. This approach may be highly misleading as interactions between Cd and other substances, e.g. various ions or inherent soil components often strongly modify Cd toxicity. Hence, we compared the toxic effect of Cd to small heterotrophic protists in soil microcosms and liquid culture. We also evaluated how zinc (Zn) affects Cd toxicity, as Zn usually accompanies Cd in a ratio of c. 100:1, and is known to impede Cd toxicity. In the soil microcosms, we also monitored the primary food source of the protists, i.e. culturable bacteria, and used soil respiration as a proxy of soil functioning. Finally, we examined to what extent Cd actually sorbs to soil. We found 1) that c. 103 times more Cd was required to obtain the same effect in the soil microcosms compared to the liquid culture, 2) that soil sorption explains why Cd, even though highly toxic in aqueous solutions, has very limited effect when applied to soil, and 3) (very surprisingly) that in our experimental systems Zn was as toxic as Cd. Our study suggests that Cd toxicity to soil protists will be small because most Cd in soil will be sorbed to the soil matrix and because the Zn:Cd ratio of 100:1 in most substances, incl. pollutants, will mean that lethal Zn effects will occur before Cd reaches toxic levels.

Microplastic and soil protists: A call for research

Microplastic is an emerging contaminant of concern in soils globally, probably gradually increasing in soil due to slow degradation. Few studies on microplastic effects on soil biota are available, and no study in a microplastic contamination context has specifically addressed soil protists. Soil protists, a phylogenetically and functionally diverse group of eukaryotic, unicellular soil organisms, are major consumers of bacteria in soils and are potentially important vehicles for the delivery of microplastics into the soil food chain. Here we build a case for focusing research on soil protists by drawing on data from previous, older studies of phagocytosis in protist taxa, which have long made use of polystyrene latex beads (microspheres). Various soil-borne taxa, including ciliates, flagellates and amoebae take up microplastic beads in the size range of a few micrometers. This included filter feeders as well as amoebae which engulf their prey. Discrimination in microplastic particle uptake depended on species, physiological state as well as particle size. Based on the results of the studies we review here, there is now a need to study microplastic effects in a pollution ecology context: this means considering a broad range of particle types under realistic conditions in the soil, and exploring longer-term effects on soil protist communities and functions.

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities

Soil protists, critical components of the soil microbiome and useful bio-indicators for soil quality, are often overlooked in microbial ecology. Here, a long-term field experiment with a cucumber monoculture was adopted to disentangle the influence of Trichoderma-enriched bio-fertilizers (BF) and organic fertilizers (OF) on the soil protists compared with that of chemical fertilizers (CF) without extra microbial inoculation. The results showed CF application was associated with lower protist richness and diversity than applications of and BF in both bulk and rhizosphere soils. Principal coordinate analysis revealed significant differences in the bulk and rhizosphere soil protist community structures, and the structures from CF treatment were obviously distinct from those resulting from OF and BF treatments in both bulk and rhizosphere soils. Moreover, in bulk soils, OF had higher relative abundances of Alveolata, Amoebozoa, Archaeplastida and Opisthokonta than did CF and BF. Compared with rhizosphere soils, Alveolata and Amoebozoa increased in bulk soil with CF, while the latter group decreased with OF. The most abundant OTUs were assigned to functional groups, and it was found that omnivores were on average, but not significantly, more abundant in bulk soil compared to rhizospheres. OTU_144 (Acanthamoebidae arachisporum) increased while OTU_54 (Hypotrichia, belonging to omnivores) decreased from bulk to rhizosphere soils in all treatments. Overall, we conclude that soil management strategies such as organic amendments can greatly alter the bulk soil protist community and that plants can further select protist community in the rhizosphere with potential consequences for plant growth in agricultural systems.

The Hidden Diversity of Flagellated Protists in Soil

Protists are among the most diverse and abundant eukaryotes in soil. However, gaps between described and sequenced protist morphospecies still present a pending problem when surveying environmental samples for known species using molecular methods. The number of sequences in the molecular PR2 database (∼130,000) is limited compared to the species richness expected (>1 million protist species) - limiting the recovery rate. This is important, since high throughput sequencing (HTS) methods are used to find associative patterns between functional traits, taxa and environmental parameters. We performed HTS to survey soil flagellates in 150 grasslands of central Europe, and tested the recovery rate of ten previously isolated and cultivated cercomonad species, among locally found diversity. We recovered sequences for reference soil flagellate species, but also a great number of their phylogenetically evaluated genetic variants, among rare and dominant taxa with presumably own biogeography. This was recorded among dominant (cercozoans, Sandona), rare (apusozoans) and a large hidden diversity of predominantly aquatic protists in soil (choanoflagellates, bicosoecids) often forming novel clades associated with uncultured environmental sequences. Evaluating the reads, instead of the OTUs that individual reads are usually clustered into, we discovered that much of this hidden diversity may be lost due to clustering.

Discrepancies Between Molecular and Morphological Databases of Soil Ciliates Studied for Temperate Grasslands of Central Europe

By measuring the change in soil protist communities, the effect of human land use on grasslands can be monitored to promote sustainable ecosystem functioning. Protists form the active link in the rhizosphere between the plant roots and higher trophic organisms; however, only few morphological species and their ecological values have yet been described in this context. To investigate the communicability between morphological and molecular databases used in the molecular barcoding of protists and in the biomonitoring of grassland soil, the present high-throughput sequencing (HTS) study (N=150) covered the area of central Europe (mesoscale) known to be well studied for ciliated protists. HTS delivered 2,404 unique reads identifying taxa in all major ciliophoran classes but exact reference matches were few. The study identified clear discrepancies between databases for well-studied taxa, where molecular databases contained multiple gene variants for single morphospecies of dominant taxa. Gene variants presented own biogeography - the eukaryotic microdiversity along gradients (e.g., land-use intensity, soil water). It is possible that many of the so called novel phylogenetic lineages and hidden diversity pointed out in environmental surveys could be evidence for the severe lack of molecular data for already known and morphologically described species, present in morphological databases.