Planktonic Ciliate Species Diversity as an Integral Component of Ecosystem Function in a Freshwater Pond

Turtle species and ecology drive carapace microbiome diversity in three seasonally interconnected wetland habitats

Different species of freshwater turtles exhibit primary behaviours ranging from aerial basking to benthic bottom-walking, cycle between wet and dry conditions at different time intervals, and undertake short-distance overland movements between aquatic habitats. These behaviours in turn may impact the accumulation of microbes on external shell surfaces of turtles and provide novel niches for differentiation of microbial communities. We assessed microbial diversity using 16S and 18S rRNA metabarcoding on carapace surfaces of six species of freshwater turtles residing in three adjacent and seasonally interconnected wetland habitats in southeast Oklahoma (United States). Communities were highly diverse, with nearly 4200 prokaryotic and 500 micro-eukaryotic amplicon sequence variants recovered, and included taxa previously reported as common or differentially abundant on turtle shells. The 16S rRNA alpha diversity tended to be highest for two species of benthic turtles, while 18S rRNA alpha diversity was highest for two basking and one shallow-water benthic species. Beta diversity of communities was more strongly differentiated by turtle species than by collection site, and ordination patterns were largely reflective of turtle species' primary habits (i.e. benthic, basking, or benthic-basking). Our data support that freshwater turtles could play a role in microbial ecology and evolution in freshwater habitats and warrant additional exploration including in areas with high native turtle diversity and inter-habitat turtle movements.

Seasonal Patterns of Phytoplankton Taxon Richness in Lakes: Effects of Temperature, Turnover and Abundance

Species richness is a key ecological characteristic that influences numerous ecosystem functions. Here we analyse the patterns and possible causes of phytoplankton taxon richness in seasonal datasets from twenty contrasting lakes in the English Lake District over six years and near-weekly datasets over 33 years from Windermere. Taxon richness was lowest in winter and highest in summer or autumn in all of the lakes. Observed richness was very similar to richness estimated from coverage and sampling effort, implying that it closely reflected true seasonal patterns. Summer populations were dominated by Chlorophyta and functional groups X1, F, N and P (sensu Reynolds). In Windermere, weekly taxon richness was strongly positively correlated with surface water temperature, as was the number of functional groups and the number of taxa per functional group. Turnover in richness of taxa and functional groups were positively correlated and both were related to surface temperature. This suggests that high taxon richness in summer is linked to higher water temperature, promoting a turnover in richness of taxa and functional groups in these lakes. However, since the number of taxa per unit concentration of chlorophyll a decreased with increasing concentration of chlorophyll a, competition might occur when abundance is high.

The Extraordinarily Rare Ciliate Legendrea loyezae Fauré-Fremiet, 1908 (Haptoria, Ciliophora)

Diverse and dynamic communities of ciliates and other microbes thrive in the natural environment, driving the functioning of aquatic ecosystems. Many microbes are present in very low numbers or are dormant in the 'seedbank', escaping detection in environmental surveys and, consequently, remaining underexplored. Here, we report an extraordinarily rare ciliate that was discovered after persistent exploration of freshwater anoxic sediments - Legendrea loyezae Fauré-Fremiet, 1908, a member of the Family Spathidiidae, Order Haptorida. In this study, we present the sixth account of the ciliate since 1908 and reveal its phylogenetic position with the first 18S rRNA data for the genus. We explain the key morphological features of the species, describing a remarkable behaviour in which the ciliate "shapeshifts'' due to its ability of controlled full extension and retraction of its tube-like tentacles. Our results shed light on the similarity of L. loyezae to another ciliate that was first described as Legendrea bellerophon, later moved under a new genus and named Thysanomorpha bellerophon. We question the validity of this taxonomic decision and, based on morphological characters and tentacle movement, we propose moving T. bellerophon back under Legendrea. This study demonstrates how continued and persistent exploration of natural habitats lead to the discovery of microbial communities and species.

A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts

Oxygenic photosynthesizers (cyanobacteria and eukaryotic algae) have repeatedly become endosymbionts throughout evolution. In contrast, anoxygenic photosynthesizers (e.g., purple bacteria) are exceedingly rare as intracellular symbionts. Here, we report on the morphology, ultrastructure, lifestyle, and metagenome of the only "purple-green" eukaryote known. The ciliate Pseudoblepharisma tenue harbors green algae and hundreds of genetically reduced purple bacteria. The latter represent a new candidate species of the Chromatiaceae that lost known genes for sulfur dissimilation. The tripartite consortium is physiologically complex because of the versatile energy metabolism of each partner but appears to be ecologically specialized as it prefers hypoxic sediments. The emergent niche of this complex symbiosis is predicted to be a partial overlap of each partners' niches and may be largely defined by anoxygenic photosynthesis and possibly phagotrophy. This purple-green ciliate thus represents an extraordinary example of how symbiosis merges disparate physiologies and allows emergent consortia to create novel ecological niches.

Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms

The pelagic / anoxic hypolimnion population of Spirostomum teres was investigated as a part of the long-term ciliates’ monitoring (2003–2016) in an oligo- to mesotrophic monomictic hyposaline crater lake Alchichica (Puebla / Veracruz, Mexico), including an analysis of picoplankton (both heterotrophic, HPP and autotrophic, APP) and inorganic compounds of nitrogen (ammonium, nitrite, nitrate), phosphorus (dissolved reactive phosphorus, DRP) and silicon. Additionally, detailed studies of the ciliate vertical distribution and feeding activity measured upon fluorescently labelled APP (picocyanobacteria) were carried out. The results were compared with those from a neighbour freshwater crater lake La Preciosa and with a meromictic karstic lake La Cruz (Cuenca, Spain). The ciliate vertical distribution within the water column was very well defined: During the first decade, the benthic population was frequently found throughout a developing stratification of the lake. The established stratification of the lake turned the conditions favourable for the formation of an oxycline / hypolimnion population, typically, several meters below the deep chlorophyll maximum (formed basically by diatoms); the population preferred the layers without detectable dissolved oxygen. However, an observed gradient of light (PAR) could support both oxygenic and anoxygenic photosynthesis. Late stratification after deepening of the thermocline reduced the layers with S. teres population to a minimum apparently due to the drastic change in physicochemical conditions within a metalimnion, coupled with an oxycline, and limited to 1 to 2 meters; microstratification was found. Last years, the very bottom population disappeared or it was reduced and the late stratification S. teres peaks were smaller or did not appeared. Generally, S. teres oxycline / anoxic hypolimnion population was observed from June through November. Optimum picoplankton numbers in conditions that supported the ciliate growth were found: The ciliate was peaking at APP of 0.6 to 1 × 105 cells mL–1; the optimum of HPP was observed round 1.4 × 106 cells mL–1. S. teres was efficiently feeding upon picocyanobacteria in numbers of 105 cells mL–1 reaching the clearance rate of 2000 nL cell–1h–1, which represented in average 130 to 210 cells cell–1h–1 ingested. Feeding upon purple sulphur bacteria was observed but only during the end of the lake stable stratification when the ciliate population was already dropping. On the other hand, the volume specific clearance of S. teres upon picocyanobacteria (103 h–1) did not support the hypothesis that they could serve as a sole prey. Feeding upon eukaryote phytoplankton (chlorophytes Monoraphidium minutum, diatoms Cyclotella choc tawhatcheeana) could be of higher importance that previously supposed. Additionally, a use of ingested and retained photosynthetic prokaryotes is hypothesized.

Toxicity of nickel to tropical freshwater and sediment biota: A critical literature review and gap analysis

More than two-thirds of the world's nickel (Ni) lateritic deposits are in tropical regions, and just less than half are within South East Asia and Melanesia (SEAM). With increasing Ni mining and processing in SEAM, environmental risk assessment tools are required to ensure sustainable development. Currently, there are no tropical-specific water or sediment quality guideline values for Ni, and the appropriateness of applying guideline values derived for temperate systems (e.g., Europe) to tropical ecosystems is unknown. Databases of Ni toxicity and toxicity tests for tropical freshwater and sediment species were compiled. Nickel toxicity data were ranked, using a quality assessment, identifying data to potentially use to derive tropical-specific Ni guideline values. There were no data for Ni toxicity in tropical freshwater sediments. For tropical freshwaters, of 163 Ni toxicity values for 40 different species, high-quality chronic data, based on measured Ni concentrations, were found for just 4 species (1 microalga, 2 macrophytes, and 1 cnidarian), all of which were relevant to SEAM. These data were insufficient to calculate tropical-specific guideline values for long-term aquatic ecosystem protection in tropical regions. For derivation of high-reliability tropical- or SEAM-specific water and sediment quality guideline values, additional research effort is required. Using gap analysis, we recommend how research gaps could be filled. Environ Toxicol Chem 2018;37:293-317. © 2017 SETAC.

Sequestered organelles sustain aerobic microbial life in anoxic environments

We report aerobic eukaryotic microbial life in the dimly lit anoxic water layer of a small freshwater lake. The microbial eukaryote is the ciliated protozoon Histiobalantium natans. Electron microscopy of thin sections shows that the cytoplasm of the ciliate harbours sequestered chloroplasts and sequestered mitochondria. The sequestered chloroplasts are attached or in very close proximity to the ciliate's own mitochondria. The sequestered mitochondria also seem to be associated with host-ciliate mitochondria. We suggest that the oxygenic photosynthetic activity of sequestered chloroplasts, perhaps enhanced by respiration in sequestered mitochondria, contributes to servicing the respiratory oxygen requirements of the ciliate host in its anoxic habitat. Our observations are novel, with the discovery of an aerobic microbial eukaryote capable of thriving and completing its life cycle in an anoxic environment, fuelled by oxygen generated by sequestered chloroplasts. The acknowledged flexibility and functional diversity within eukaryotic microbial communities still have many secrets to release.

Oxygen and the spatial structure of microbial communities

Oxygen has two faces. On one side it is the terminal electron acceptor of aerobic respiration - the most efficient engine of energy metabolism. On the other hand, oxygen is toxic because the reduction of molecular O2 creates reactive oxygen species such as the superoxide anion, peroxide, and the hydroxyl radical. Probably most prokaryotes, and virtually all eukaryotes, depend on oxygen respiration, and we show that the ambiguous relation to oxygen is both an evolutionary force and a dominating factor driving functional interactions and the spatial structure of microbial communities.We focus on microbial communities that are specialised for life in concentration gradients of oxygen, where they acquire the full panoply of specific requirements from limited ranges of PO2, which also support the spatial organisation of microbial communities. Marine and lake sediments provide examples of steep O2 gradients, which arise because consumption or production of oxygen exceeds transport rates of molecular diffusion. Deep lakes undergo thermal stratification in warm waters, resulting in seasonal anaerobiosis below the thermocline, and lakes with a permanent pycnocline often have permanent anoxic deep water. The oxycline is here biologically similar to sediments, and it harbours similar microbial biota, the main difference being the spatial scale. In sediments, transport is dominated by molecular diffusion, and in the water column, turbulent mixing dominates vertical transport. Cell size determines the minimum requirement of aerobic organisms. For bacteria (and mitochondria), the half-saturation constant for oxygen uptake ranges within 0.05-0.1% atmospheric saturation; for the amoeba Acanthamoeba castellanii it is 0.2%, and for two ciliate species measuring around 150 microm, it is 1-2 % atmospheric saturation. Protection against O2 toxicity has an energetic cost that increases with increasing ambient O2 tension. Oxygen sensing seems universal in aquatic organisms. Many aspects of oxygen sensing are incompletely understood, but the mechanisms seem to be evolutionarily conserved. A simple method of studying oxygen preference in microbes is to identify the preferred oxygen tension accumulating in O2 gradients. Microorganisms cannot sense the direction of a chemical gradient directly, so they use other devices to orient themselves. Different mechanisms in different prokaryotic and eukaryotic microbes are described. In O2 gradients, many bacteria and protozoa are vertically distributed according to oxygen tension and they show a very limited range of preferred PO2. In some pigmented protists the required PO2 is contingent on light due to photochemically generated reactive oxygen species. In protists that harbour endosymbiotic phototrophs, orientation towards light is mediated through the oxygen production of their photosynthetic symbionts. Oxygen plays a similar role for the distribution of small metazoans (meiofauna) in sediments, but there is little experimental evidence for this. Thus the oxygenated sediments surrounding ventilated animal burrows provide a special habitat for metazoan meiofauna as well as unicellular organisms.

Oxygen sensing drives predictable migrations in a microbial community

Oxygen sensing is widely practised by aerobic organisms ranging from bacteria to vertebrates, and a dominant oxygen-sensing mechanism may persist among all aerobes. We traced population migrations of 10 species of the larger aerobic ciliated protozoa living in lake sediment, and in the 15 m water column of Esthwaite Water in the English Lake District (UK). In so doing, we discovered that the character and dynamics of the lake sediment and water column were remarkably predictable in performance over a continuous period of almost 2 years. Increasing warming of the lake sediment, coupled with low oxygen tension, resulted in the emergence of aerobic ciliates out of the sediment and their migration into the water column. And with the annual collapse of thermal stratification in the water column, the whole annual cycle was repeated. In an unusual discovery, we found that particular ciliate species seemed to be 'linked' to other (functionally different) ciliate species partners via the ambient oxygen tension. The favoured hypothesis is that all ciliate species in a particular body-size range seek out a particular, preferred oxygen tension. If that is the case, the 'cement' providing the cohesion of the ciliate community might actually be the preferred oxygen tension. The principal aim of our study is to clarify the microbial migration itself, not the response of the different ciliate species to oxygen gradients once they have established themselves in the water column. The latter happens once the organisms have migrated out of the sediment together, driven by the ambient oxygen tension.

SPECIES DIVERSITY MODULATES PREDATION

Predation occurs in a context defined by both prey and non-prey species. At present it is largely unknown how species diversity in general, and species that are not included in a predator's diet in particular, modify predator-prey interactions. Therefore we studied how both the density and diversity of non-prey species modified predation rates in experimental microcosms. We found that even a low density of a single nonprey species depressed the asymptote of a predator's functional response. Increases in the density and diversity of non-prey species further reduced predation rates to very low levels. Controls showed that this diversity effect was not due to the identity of any of the non-prey species. Our results establish that both the density and diversity of species outside a predator's diet can significantly weaken the strength of predator-prey interactions. These results have major implications for ecological theory on species interactions in simple vs. complex communities. We discuss our findings in terms of the relationship between diversity and stability.

Protist taxonomy: an ecological perspective

This is an exploration of contemporary protist taxonomy within an ecological perspective. As it currently stands, the 'morphospecies' does not accommodate the information that might support a truly ecological species concept for the protists. But the 'morphospecies' is merely a first step in erecting a taxonomy of the protists, and it is expected to become more meaningful in the light of genetic, physiological and ecological research in the near future. One possible way forward lies in the recognition that sexual and asexual protists may all be subject to forces of cohesion that result in (DNA) sequence-similarity clusters. A starting point would then be the detection of 'ecotypes'--where genotypic and phenotypic clusters correspond; but for that we need better information regarding the extent of clonality in protists, and better characterization of ecological niches and their boundaries. There is some progress with respect to the latter. Using the example of a community of ciliated protozoa living in the stratified water column of a freshwater pond, it is shown to be possible to gauge the potential of protists to partition their local environment into ecological niches. Around 40 morphospecies can coexist in the superimposed water layers, which presumably represent different ecological niches, but we have yet to discover if these are discrete or continuously variable. It is a myth that taxonomic problems are more severe for protists than for animals and plants. Most of the fundamental problems associated with species concepts (e.g. asexuals, sibling species, phenotypic variation) are distributed across biota in general. The recent history of the status of Pfiesteria provides a model example of an integrated approach to solving what are essentially taxonomic problems.

Cryptic freshwater ciliates in a hypersaline lagoon

Ubiquitous dispersal of free-living microbial species implies that each and every ecosystem supports a 'seedbank' of microbial species that are imported by random dispersal. However, many of the microbial species present in any particular ecosystem will probably never thrive there because the local environment is unsuitable for their population growth. To test this, we investigated the ciliated protozoa in a hypersaline lagoon in Almeria, Spain, using selective enrichment to reveal typical freshwater species, as the 'signature' of random dispersal. Twenty-four ciliate species, 14 of them not previously recorded from hypersaline waters, were identified in the undiluted waters of the lagoon. But when the salinity was gradually diluted, further species typical of fresh- and brackish waters emerged, indicating that they had persisted in a viable state at the previously high salinity. These additional species increased the recorded ciliate species total for the lagoon to 36. The species found in the lagoon appeared to be adapted to either high, or variable, or low salinity, implying that they may have originated in a variety of habitats that differed greatly with respect to salinity regime.

Ciliate populations in temporary freshwater ponds: seasonal dynamics and influential factors

SUMMARY 1. The ciliate populations of two temporary ponds in southern Ontario were studied throughout their aquatic phases in 2001. Pond I (∼1 ha) held water for 98 days, whereas Pond II (∼0.25 ha) held water for 34 days. Populations were assessed both within the ponds themselves and within a series of enclosures in which invertebrate predator pressure was manipulated. 2. In the natural pond water, total ciliate abundance in Pond II rose rapidly from day 1 increasing two orders of magnitude by day 7. In contrast, total abundance in Pond I began at the same level as in Pond II but increased much more slowly, reached a plateau of around 500 individuals L^-1, and increased again late in the hydroperiod. 3. Despite being only 500 m apart, the two ponds were fairly dissimilar in terms of their species richness and species composition. Pond I contained 50 species compared with 70 species for Pond II, with only 24 species shared. Additional species occurred within the enclosures raising the total species richness to 145 species; 88 from Pond I, 104 from Pond II, with 47 species (30%) in common. Pond II contained more mid-sized ciliates (50-200 μm), whereas Pond I was dominated by smaller ciliates, especially in mid-May and early June. In Pond I, cumulative species richness throughout the hydroperiod was highest in the predator addition enclosures (65 ± 4 species), followed by the partial-predator exclusion enclosures (50 ± 4). Lowest species richness was found in the control enclosures (39 ± 2) and in the pondwater controls (39 ± 0). Differences between the ciliates in the natural pond water and the enclosures appeared to be related to a greater concentration of phytoplankton within the enclosures (perhaps resulting from extensive growth of duckweed, Lemna, outside), and higher densities of zooplankters in the pond. 4. The physicochemical environment influenced species richness, total abundance and the number of rare species (27 in Pond II versus 13 in Pond I). Variation in ciliate abundance in Pond I could be explained by the number of days after filling (39%) and enclosure treatment (23%). These two parameters also explained 72% of the variation in species richness in Pond I (46 and 26%, respectively). Sixty-five per cent of the variation in abundance in Pond II could be explained by the measured parameters: number of days after filling 27%, pH 19%, and nitrate levels 12%. Fifty-two per cent of the variation in species richness was explained by the environmental parameters, of which pH was the most influential. Species succession was a strong feature of both ponds and its relationship to environmental variables and the presence of other organisms is discussed. 5. Addition of invertebrate predators resulted in higher abundance and higher species richness for a limited time period in one of the ponds - suggesting that differences in foodweb dynamics may influence ciliate community composition.

Apparent global ubiquity of species in the protist genus Paraphysomonas

Evidence is presented for the ubiquity of protist species. Using the example of protists that leave traces (siliceous scales) of their recent population growth, we show that most - perhaps all species in the genus Paraphysomonas, are ubiquitous. Of the species recorded in surveys carried out worldwide, we have identified 78% of their number in 0.1 cm2 of sediment collected from a freshwater pond (total area 10(8) cm2) in England. Moreover, the pond appears to act like a microcosm of aquatic environments in general, for species that are globally rare or abundant, are likewise rare or abundant in the pond. We assume that the rate of neutral migration to the pond is greatest for the globally abundant species. As these species are probably capable of growth in a broad range of conditions, they will more frequently encounter the environment they require for population growth. Thus globally abundant species are also locally abundant in the pond - a pattern that will be amplified by periodic cyst production. Ubiquitous dispersal is probably driven by very high absolute abundance of individuals, and the water column of the pond was estimated to support >10(14) Paraphysomonas individuals. Ubiquity will dampen rates of speciation, and the evidence presented here indicates that global species richness of Paraphysomonas is indeed modest - perhaps close to what is already known.