Redescription of the enigmatic myriapod Hanseniellachilensis (Hansen, 1903) (Symphyla, Scutigerellidae) based on scanning electron microscope images of Chilean specimens.

Hanseniellachilensis is the only myriapod of the class Symphyla known from Chile. This garden centipede, or pseudocentipede, was described more than 120 years ago based on morphologically incomplete specimens collected in central Chile, a well-known biodiversity hotspot. In this study, we redescribe this species based on morphologically complete specimens collected near the type locality using scanning electron microscope images. Our study provides the description of diagnostic characters hitherto unknown in this species such as macrochaetae of the tergites and spinnerets of the cerci. We also include a new record from central Chile and discuss the presumed presence of this species in Argentina and Madagascar.

Checklist, diversity and biogeography of ciliates (Ciliophora) from Chile.

There is a significant gap in research and knowledge on the diversity and distribution of Chilean ciliates. To tackle these issues, we used cultures and protargol preparations to describe the ciliates present in poorly explored areas. At these sites, we identified 45 ciliate morphospecies, 35 of which represent unprecedent records to Chile. Then, we brought together our records with literature data to construct a species checklist. This checklist summarises 132 years of data and describes the identity, habitat and distribution of 207 species, including 15 species potentially endemic to Chile. This checklist is far from complete: a diversity estimate suggests that at least two-thirds of the ciliate species occurring in Chile have yet to be described. The checklist is dominated by freshwater taxa because ciliates from marine, brackish and terrestrial environments have rarely been investigated in Chile. Finally, after controlling for sampling artefacts, we found that ciliates exhibit a bell-shaped latitudinal diversity gradient in Chile. This peculiar biogeographical pattern is common in Chile. Plants, animals and testate amoebae also exhibit a bell-shaped latitudinal diversity gradient in Chile. This finding suggests that the historical contingencies that drove the biogeography of the Chilean biota also shaped ciliate biogeography.

Niche Conservatism Drives the Elevational Diversity Gradient in Major Groups of Free-Living Soil Unicellular Eukaryotes.

Ancestral adaptations to tropical-like climates drive most multicellular biogeography and macroecology. Observational studies suggest that this niche conservatism could also be shaping unicellular biogeography and macroecology, although evidence is limited to Acidobacteria and testate amoebae. We tracked the phylogenetic signal of this niche conservatism in far related and functionally contrasted groups of common soil protists (Bacillariophyta, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida) along a humid but increasingly cold elevational gradient in Switzerland. Protist diversity decreased, and the size of the geographic ranges of taxa increased with elevation and associated decreasing temperature (climate), which is consistent with a macroecological pattern known as the Rapoport effect. Bacillariophyta exhibited phylogenetically overdispersed communities assembled by competitive exclusion of closely related taxa with shared (conserved) niches. By contrast, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida exhibited phylogenetically clustered communities assembled by habitat filtering, revealing the coexistence of closely related taxa with shared (conserved) adaptations to cope with the humid but temperate to cold climate of the study site. Phylobetadiversity revealed that soil protists exhibit a strong phylogenetic turnover among elevational sites, suggesting that most taxa have evolutionary constraints that prevent them from colonizing the colder and higher sites of the elevation gradient. Our results suggest that evolutionary constraints determine how soil protists colonize climates departing from warm and humid conditions. We posit that these evolutionary constraints are linked to an ancestral adaptation to tropical-like climates, which limits their survival in exceedingly cold sites. This niche conservatism possibly drives their biogeography and macroecology along latitudinal and altitudinal climatic gradients.

Macronuclear Plasticity in Two South American Populations of Spirostomum (Ciliophora, Heterotrichea) Warns About its Use for Species Classification: Revision and New Insights.

Spirostomum is a widely distributed heterotrichean genus composed of well-known species with described ecology and phylogenetic affinities. The morphological classification of Spirostomum species is mostly based on the body size/shape, number of cortical granule rows and macronuclear characteristics. These features along with molecular phylogenies based on ribosomal genes divide the genus into two phylogroups, one including species with a compact macronucleus, and another including species with a moniliform macronucleus. Here, we present our observations on atypical Spirostomum specimens with unusually two distinct macronuclei and shortened adoral zone of membranelles. These atypical forms appeared in the cultures of S. minus and S. yagiui, sampled at different sites in South America (Chile and Brazil) and associated with unrelated substrate types. Morphological observations of living and stained cells, 18S rRNA gene analyses, and a thorough investigation of the literature suggest that the atypical phenotype may be a result of uncommon pathways during the conjugative process. Thus, we demonstrate that studies of ciliate natural populations and their morphological variations, especially from undersampled biogeographical regions, can reveal the boundaries of widely used morphological characters for Spirostomum taxonomy and species identification.

Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists.

Recent studies show that soil eukaryotic diversity is immense and dominated by micro-organisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to micro-organisms. Major diversification events in multicellular organisms have often been attributed to long-term climatic and geological processes, but the impact of such processes on protist diversity has received much less attention as their distribution has often been believed to be largely cosmopolitan. Here, we quantified phylogeographical patterns in Hyalosphenia papilio, a large testate amoeba restricted to Holarctic Sphagnum-dominated peatlands, to test if the current distribution of its genetic diversity can be explained by historical factors or by the current distribution of suitable habitats. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the H. papilio complex, and was lower in Eurasia despite extensive suitable habitats. These results suggest that patterns of phylogenetic diversity and distribution can be explained by the history of Holarctic Sphagnum peatland range expansions and contractions in response to Quaternary glaciations that promoted cladogenetic range evolution, rather than the contemporary distribution of suitable habitats. Species distributions were positively correlated with climatic niche breadth, suggesting that climatic tolerance is key to dispersal ability in H. papilio. This implies that, at least for large and specialized terrestrial micro-organisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographical patterns and may partly explain their very high overall diversity.

Genetic Diversity and Distribution of Blastocystis Subtype 3 in Human Populations, with Special Reference to a Rural Population in Central Mexico.

Blastocystis subtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity of Blastocystis ST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations of Blastocystis ST3 from other regions of the planet. Our analyses reveled that diversity of Blastocystis ST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a common widespread haplotype from which the others were generated recently. Finally, our results suggested a recent expansion of the diversity of Blastocystis ST3 worldwide.

Soil protists: a fertile frontier in soil biology research.

Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.

Environmental filtering and phylogenetic clustering correlate with the distribution patterns of cryptic protist species.

The community composition of any group of organisms should theoretically be determined by a combination of assembly processes including resource partitioning, competition, environmental filtering, and phylogenetic legacy. Environmental DNA studies have revealed a huge diversity of protists in all environments, raising questions about the ecological significance of such diversity and the degree to which they obey to the same rules as macroscopic organisms. The fast-growing cultivable protist species on which hypotheses are usually experimentally tested represent only a minority of the protist diversity. Addressing these questions for the lesser known majority can only be inferred through observational studies. We conducted an environmental DNA survey of the genus Nebela, a group of closely related testate (shelled) amoeba species, in different habitats within Sphagnum-dominated peatlands. Identification based on the mitochondrial cytochrome c oxidase 1 gene, allowed species-level resolution as well as phylogenetic reconstruction. Community composition varied strongly across habitats and associated environmental gradients. Species showed little overlap in their realized niche, suggesting resource partitioning, and a strong influence of environmental filtering driving community composition. Furthermore, phylogenetic clustering was observed in the most nitrogen-poor samples, supporting phylogenetic inheritance of adaptations in the group of N. guttata. This study showed that the studied free-living unicellular eukaryotes follow to community assembly rules similar to those known to determine plant and animal communities; the same may be true for much of the huge functional and taxonomic diversity of protists.

Geographical distance and local environmental conditions drive the genetic population structure of a freshwater microalga (Bathycoccaceae; Chlorophyta) in Patagonian lakes.

The patterns and mechanisms underlying the genetic structure of microbial populations remain unresolved. Herein we investigated the role played by two non-mutually exclusive models (i.e. isolation by distance and isolation by environment) in shaping the genetic structure of lacustrine populations of a microalga (a freshwater Bathycoccaceae) in the Argentinean Patagonia. To our knowledge, this was the first study to investigate the genetic population structure in a South American microorganism. Population-level analyses based on ITS1-5.8S-ITS2 sequences revealed high levels of nucleotide and haplotype diversity within and among populations. Fixation index and a spatially explicit Bayesian analysis confirmed the occurrence of genetically distinct microalga populations in Patagonia. Isolation by distance and isolation by environment accounted for 38.5% and 17.7% of the genetic structure observed, respectively, whereas together these models accounted for 41% of the genetic differentiation. While our results highlighted isolation by distance and isolation by environment as important mechanisms in driving the genetic population structure of the microalga studied, none of these models (either alone or together) could explain the entire genetic differentiation observed. The unexplained variation in the genetic differentiation observed could be the result of founder events combined with rapid local adaptations, as proposed by the monopolisation hypothesis.

First freshwater member ever reported for the family Bathycoccaceae (Chlorophyta; Archaeplastida) from Argentinean Patagonia revealed by environmental DNA survey.

We characterized molecularly the first freshwater member ever reported for the family Bathycoccaceae in Lake Musters (Argentinean Patagonia). Members of this family are extremely numerous and play a key ecological role in marine systems as primary producers. We cloned a fragment comprising the SSU rRNA gene+ITS region from environmental DNA using specific mamiellophyte primers. The unique SSU rRNA gene sequence obtained clustered robustly with Bathycoccus prasinos. Analysis of the two-dimensional structure of the ITS region showed the presence of a typical supplementary helix in the ITS-2 region, a synapomorphy of Bathycoccaceae, which confirmed further its phylogenetic placement. We finally discuss the possible causes for the presence of this organism in Lake Musters.

Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes.

Microbial eukaryotes play important roles in aquatic ecosystem functioning. Unravelling their distribution patterns and biogeography provides important baseline information to infer the underlying mechanisms that regulate the biodiversity and complexity of ecosystems. We studied the distribution patterns and factors driving diversity gradients in microeukaryote communities (total, abundant, uncommon and rare community composition) along a latitudinal gradient of lakes distributed from Argentinean Patagonia to Maritime Antarctica using both denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (Illumina HiSeq). DGGE and abundant Illumina operational taxonomic units (OTUs) showed both decreasing richness with latitude and significant differences between Patagonian and Antarctic lakes communities. In contrast, total richness did not change significantly across the latitudinal gradient, although evenness and diversity indices were significantly higher in Patagonian lakes. Beta-diversity was characterized by a high species turnover, influenced by both environmental and geographical descriptors, although this pattern faded in the rare community. Our results suggest the co-existence of a 'core biosphere' containing reduced number of abundant/dominant OTUs on which classical ecological rules apply, together with a much larger seedbank of rare OTUs driven by stochastic and reduced dispersal processes. These findings shed new light on the biogeographical patterns and forces structuring inland microeukaryote composition across broad spatial scales.

Cinderella's helping pigeons of the microbial world: The potential of testate amoebae for identifying cryptotephra.

Cryptotephra (particles <125µm) is a key record for monitoring past and current volcanic activity. However, its extraction from the host sediment and analysis is often long and difficult because of its small size. Finding a simple method to extract cryptotephra from environmental samples would therefore make its analysis much easier. We hypothesized that arcellinid testate amoebae may hold such a potential. These free-living shelled protists are among the earliest microorganisms to colonize volcanic tephra, and build their shell by agglutinating minerals from their environment. We analyzed by X-ray Spectrometry the mineral signature of tephra from the 2011 Puyehue-Cordon Caulle Volcanic Complex (Chile) eruption ash fallout and compared it to that of the shells of 51 individual testate amoebae (three individuals from each of 17 species) from 13 samples collected at different distances from the active vent. The mineral composition of particles within shells closely matched that of similar size class particles from their environment. The capacity of testate amoebae to randomly use mineral grains from their environment makes it possible to use their shells to assess the mineral composition of cryptotephra from soil, peat or sediment samples. Testate amoebae therefore represent the microbial world's version of Cinderella's helping pigeons.

Checklist, diversity and distribution of testate amoebae in Chile.

Bringing together more than 170 years of data, this study represents the first attempt to construct a species checklist and analyze the diversity and distribution of testate amoebae in Chile, a country that encompasses the southwestern region of South America, countless islands and part of the Antarctic. In Chile, known diversity includes 416 testate amoeba taxa (64 genera, 352 infrageneric taxa), 24 of which are here reported for the first time. Species-accumulation plots show that in Chile, the number of testate amoeba species reported has been continually increasing since the mid-19th century without leveling off. Testate amoebae have been recorded in 37 different habitats, though they are more diverse in peatlands and rainforest soils. Only 11% of species are widespread in continental Chile, while the remaining 89% of the species exhibit medium or short latitudinal distribution ranges. Also, species composition of insular Chile and the Chilean Antarctic territory is a depauperated subset of that found in continental Chile. Nearly, the 10% of the species reported here are endemic to Chile and many of them are distributed only within the so-called Chilean biodiversity hotspot (ca. 25° S-47° S). These findings are here thoroughly discussed in a biogeographical and evolutionary context.