Unexpected biodiversity of ciliates in marine samples from below the photic zone

Marine microbial eukaryotes play critical roles in planktonic food webs and have been described as most diverse in the photic zone where productivity is high. We used high‐throughput sequencing (HTS) to analyse the spatial distribution of planktonic ciliate diversity from shallow waters (<30 m depth) to beyond the continental shelf (>800 m depth) along a 163 km transect off the coast of New England, USA. We focus on ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), as these taxa are major components of marine food webs. We did not observe the decrease of diversity below the photic zone expected based on productivity and previous analyses. Instead, we saw an increase of diversity with depth. We also observed that the ciliate communities assessed by HTS cluster by depth layer and degree of water column stratification, suggesting that community assembly is driven by environmental factors. Across our samples, abundant OTUs tend to match previously characterized morphospecies while rare OTUs are more often undescribed, consistent with the idea that species in the rare biosphere remain to be characterized by microscopy. Finally, samples taken below the photic zone also reveal the prevalence of two uncharacterized (i.e. lacking sequenced morphospecies) clades – clusters X₁ and X₂ – that are enriched within the nano‐sized fraction (2–10 μm) and are defined by deletions within the region of the SSU‐rDNA analysed here. Together, these data reinforce that we still have much to learn about microbial diversity in marine ecosystems, especially in deep‐waters that may be a reservoir for rare species and uncharacterized taxa.     

Ciliate diversity and distribution across horizontal and vertical scales in the open ocean

Ciliates are globally distributed eukaryotic organisms inhabiting virtually all environments on Earth. Although ciliates range from 10 µm to a few millimetres in cell size, they are repeatedly reported in the pico‐sized fraction (<2–3 µm) of molecular surveys. Here, we used existing data sets (BioMarKs and Tara Oceans) with different size fractions to demonstrate that the ciliate pico‐sized signal, probably derived from cell breakage during filtration, is informative and reliable to study marine ciliate biodiversity and biogeography. We then used sequences from the pico‐eukaryotic fraction of two circumnavigation expeditions, Malaspina‐2010 and Tara Oceans, to give insights into the taxonomic composition and horizontal and vertical distribution of ciliates in the global ocean. The results suggested a high homogeneity of ciliate communities along the ocean surface from temperate to tropical waters, with ciliate assemblages dominated by a few abundant and widely distributed taxa. Very few taxa were found in a single oceanic region, therefore suggesting a high level of ciliate cosmopolitanism in the global ocean. In vertical profiles, ciliates were detected up to 4,000 m depth, and a clear vertical community structuring was observed. Our results provided evidence supporting ciliates as deeply integrated organisms in the deep‐sea trophic web, where they may play a relevant role as symbionts of metazoans and grazers of prokaryotes and small eukaryotes in the water column and in aggregates.     

Protist diversity in suboxic and sulfidic waters of the Black Sea

The oxic-anoxic transition zone of the Black Sea comprises a large suboxic zone as well as anoxic and sulfidic waters. While the prokaryotes and biogeochemical cycles that characterize this zone have been frequently studied, little is known about the diversity or ecology of its microbial eukaryotes. Here, we present the first broad qualitative report of the protist species composition in the Black Sea redoxcline using molecular tools. Fingerprint analysis from the whole redoxcline revealed a complex community structure of metabolically active protists with distinct shifts along the redox gradient. Additionally, 18S rRNA gene clone libraries were used to compare protist species composition of suboxic and sulfidic water layers. Among the ciliates, sequences related to Pleuronema and Strombidium were dominant in both water layers whereas sequences affiliated with anaerobic plagiopylids and Cyclidium were detected only in the sulfidic zone. Among the flagellates, mainly stramenopiles (mostly bicosoecids and chrysophytes) occurred throughout the redoxcline. In the sulfidic zone we found stramenopile sequences but also euglenozoans, jakobids and choanoflagellates that were related to clonal sequences from other anoxic marine habitats, thus indicating the existence of globally distributed groups of anoxic flagellates. Higher species diversity in the sulfidic zone and about twice as many novel sequence types of ciliates and stramenopiles compared with the suboxic layer emphasizes the importance of anoxic, sulfidic waters as habitat for high protist diversity although the function of these organisms is yet unknown.     

Interstitial Ciliates: Benthic Microaerophiles or Planktonic Anaerobes?

We observed marine benthic interstitial ciliates Geleia sp. and Tracheloraphis sp. inhabiting the water column of a chemically stratified salt pond. This habitat is uncharacteristic for interstitial ciliates, yet they displayed active and abundant planktonic populations (up to 800 and 250 cells/liter, respectively) and a well-defined pattern of vertical distribution. Completely absent from the oxygenated epilimnion, they first appeared at the oxic/anoxic interface and were present throughout the anoxic hypolimnion. The data could not be explained by a passive removal (e.g. by currents) of these ciliates from their conventional habitat (soft sediments) to water column. The results suggest that 1) these ciliates favored an anoxic environment, and 2) they switched to a planktonic lifestyle as appropriate conditions (seasonal anoxia) developed in the water column. This sharply contrasts the classic view of these ciliates as specifically benthic and aerobic (albeit microaerophilic) organisms. We hypothesize that Geleia sp. and Tracheloraphis sp. can readily grow in either water column or benthos, but are typically found in sediments simply because they contain their preferred (anoxic) niche.     

Ecology of cavernicolous ciliates from the anchihaline lagoons of Mallorca

On the island of Mallorca, anchihaline lagoons, meromictic in character, are common in the flooded coastal karst. These subterranean lagoons, containing important populations of crustacea, maintain a connection, albeit tenuous, to the sea. Thus, the first truly quantitative study of marine ciliates inhabiting anchihaline lagoons was undertaken between April 1996 and April 1997. Physical and chemical measurements were taken in-situ, together with water samples for faunal analysis in each of four stratified lakes. These lagoons typically displayed a temperature inversion, an increase in conductivity and a decrease in dissolved oxygen concentration with depth. Ciliates were present in all lagoons studied, with a total of nine species recorded. All were assigned to known taxa. Spatial distribution of the trophic cells was noteworthy with populations clearly stratified within the water column, most being found at the waters surface, sometimes in association with rafts of floating calcite crystals, or in the sediment. Only on one occasion were ciliates recorded in mid-water. Abundance was very low, typically <1 ciliate cm^–3. The floating calcite crystals may form a delimitable biotope for ciliate populations. The role of the cyst in maintaining populations of ciliates in these cave waters is discussed.     

Microbial community development on model particles in the deep sulfidic waters of the Black Sea

Microorganisms attached to particles have been shown to be different from free-living microbes and to display diverse metabolic activities. However, little is known about the ecotypes associated with particles and their substrate preference in anoxic marine waters. Here, we investigate the microbial community colonizing particles in the anoxic and sulfide-rich waters of the Black Sea. We incubated beads coated with different substrates in situ at 1000 and 2000 m depth. After 6 h, the particle-attached microbes were dominated by Gamma- and Alpha-proteobacteria, and groups related to the phyla Latescibacteria, Bacteroidetes, Planctomycetes and Firmicutes, with substantial variation across the bead types, indicating that the attaching communities were selected by the substrate. Further laboratory incubations for 7 days suggested the presence of a community of highly specialized taxa. After incubation for 35 days, the microbial composition across all beads and depths was similar and primarily composed of putative sulfur cycling microbes. In addition to the major shared microbial groups, subdominant taxa on chitin and protein-coated beads were detected pointing to specialized microbial degraders. These results highlight the role of particles as sites for attachment and biofilm formation, while the composition of organic matter defined a secondary part of the microbial community.     

Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia

Dissolved oxygen concentration plays a major role in shaping biotic interactions and nutrient flows within marine ecosystems. Throughout the global ocean, regions of low dissolved oxygen concentration (hypoxia) are a common and expanding feature of the water column, with major feedback on productivity and greenhouse gas cycling. To better understand microbial diversity underlying biogeochemical transformations within oxygen-deficient oceanic waters, we monitored and quantified bacterial and archaeal community dynamics in relation to dissolved gases and nutrients during a seasonal stratification and deep water renewal cycle in Saanich Inlet, British Columbia, a seasonally anoxic fjord. A number of microbial groups partitioned within oxygen-deficient waters including Nitrospina and SAR324 affiliated with the δ- proteobacteria , SAR406 and γ- proteobacteria related to thiotrophic gill symbionts of deep-sea clams and mussels. Microbial diversity was highest within the hypoxic transition zone decreasing dramatically within anoxic basin waters and temporal patterns of niche partitioning were observed along defined gradients of oxygen and phosphate. These results provide a robust comparative phylogenetic framework for inferring systems metabolism of nitrogen, carbon and sulfur cycling within oxygen-deficient oceanic waters and establish Saanich Inlet as a tractable model for studying the response of microbial communities to changing levels of water column hypoxia.     

Response of endemic Clarias species’ life-history biometrics to land use around the papyrus-dominated Mpologoma riverine wetland,Uganda

Climate change may threaten the fisheries of Lake Victoria by increasing density differentials in the water column, thereby strengthening stratification and increasing the intensity and duration of deoxygenation in the deeper waters. Between 1927 and 2008 the lake's temperature increased by 0.99 °C at the surface and by 1.34 °C at depths >50 m, with the rate of warming increasing most rapidly between 2000 and 2008. In February 2000 there were marked thermal discontinuities in the water column at a number of deep stations, with marked oxyclines at depths ranging from 30–50 m, and with all stations being anoxic from 50 m downwards. In contrast, in February 2007 the lake's temperature had risen, especially at the bottom, and both the thermal discontinuities and oxyclines were much reduced, only one station recording a dissolved oxygen concentration of <2.0 mg l^–1 at 50 m. This may reflect the fact that deeper waters were warming faster, and the reasons for this are discussed. These data suggest that the impacts of warming on the thermal regime of African lakes may be highly variable and unpredictable and, in this case, may have reduced its threat to the fisheries.     

Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (2 and 50 m) and deeper layers (200 and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. The results of our study indicate that the microbial communities sampled in this study are different from those identified in water column in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea.     

Comparison of ciliate communities in the anoxic hypolimnia of three lakes: general features and the influence of lake characteristics

The ciliate communities and their food sources were investigatedin the anoxic hypolimnia of three lakes with differing waterchemistry. Bacterial biomass and, as a result, the biomass ofbactenvorous ciliates were correlated with lake trophy. Additionally,high sulfate and sulfide concentrations led to high bacterialbiomass of sulfate reducers and anaerobic phototrophic and heterotrophicbacteria, which in turn sustained large ciliate populations.The anaerobic ciliate communities of the lakes shared many characteristics.They were comprised of the same or closely related species;this was attributed to a low diversity of food sources. Ciliateto prey biomass ratios were 1.2–3.8% which is consistentwith a low theoretical growth efficiency of anaerobic metabolism.Grazing pressure on anaerobic ciliates by metazoa was insignificant.In all three lakes, ciliate populations showed distinct verticalnon-random distribution patterns which were often correlatedwith the distribution of the corresponding food sources. Itis suggested that the microbial communities in anoxic waterbodies are largely influenced by few common environmental conditionsand are therefore often inhabited by similarly structured ciliatecommunities.     

Micro-organism activity in aggregate layers in shallow eutrophic brackish water as influenced by wind induced mixing; an experimental approach

In the shallow eutrophic waters of the Darss-Zingst-ecosystem (Baltic Sea) wind induced mixing of the water column, and resuspension of sediment is an important phenomenon. Incubation experiments (7 days) with natural water were performed in the laboratory under simulated mixing conditions in order to assess the effects on abundance, biomass and activity of bacteria, heterotrophic nanoflagellates and ciliates in the water column and upper bottom layers. Under calm mixing conditions a bottom layer developed, rich in organic aggregates. Bacterial biomass increased through increase of bacteria abundance and doubled cell volume. Consequently, biomass of flagellates and, more pronounced, of ciliates increased. The bottom layer, comprising only 15% of the incubated volume, containedca. 60% of the bacterial biomass and ca. 55% of production, 75 and 95% of flagellate biomass, and ca. 70% of ciliate biomass. It is concluded that bottom layers rich in organic aggregates, although not being present permanently, play an important role in the shallow Darss-Zingst-ecosystem.     

An approach to identifying potential surrogates of periphytic ciliate communities for monitoring water quality of coastal waters

For identifying the potential surrogate of periphytic ciliate communities for monitoring marine water quality, the different taxonomic resolutions/taxa as surrogates and different data transformations were studied based on two datasets of ciliate communities in Korean coastal waters. Multivariate analyses showed that: (1) a dominant Zoothamnium duplicatum significantly masked the temporal patterns of periphytic ciliate community; (2) the order level resolution maintained sufficient information to evaluate the efficient patterns of ciliate communities in response to environmental impacts; (3) the vagile-ciliate assemblage at species-level resolution was as costly as whole periphytic ciliate communities without Z. duplicatum at the order level; and (4) the severity of data transformations played a crucial role for effectiveness of surrogates, e.g., heavy transformation for species level and mild for higher. These results suggest that the use of lower taxonomic resolutions is time-efficient and would allow improving sampling strategies of large spatial/temporal scale monitoring researches in the marine ecosystem.     

Redescription of Strombidium oculatum Gruber 1884 (Ciliophora,Oligotrichia)

The marine, tide pool-dwelling ciliate Stombidium oculatum was redescribed using live, stained, SEM, and TEM material prepared from samples collected from pools on the Isle of Man (Irish Sea) and Brittany (France). Also, we reviewed the older German and French works that reported on ciliates collected in the Mediterranean and Brittany, respectively. The Brittany and Isle of Man populations of the ciliate were considered identical. Some morphological and behavioural differences exist between the Brittany-Isle of Man populations and the Mediterranean populations, but they were insufficient to distinguish different taxa. Thus, taxa from all three locations were considered to be conspecific. Key features used to describe the ciliate were: morphology and ultrastructure of the free-swimming ciliate; cyst morphology; presence of mixotrophic-chloroplasts; presence of an eye spot composed of stigma obtained from chlorophyte prey; division, morphogenesis, and nuclear structure; live observations and behaviour, including the encystment-excystment cycle. Based on morphological and behavioural characteristics the taxon was distinguished from other similar species, and a neotype has been designated as no type material exists.     

Trophic-functional patterns of biofilm-dwelling ciliates at different water depths in coastal waters of the Yellow Sea,northern China

Vertical variations in trophic-functional patterns of biofilm-dwelling ciliates were studied in coastal waters of the Yellow Sea, northern China. A total of 50 species were identified and assigned to four trophic-functional groups (TFgrs): algivores (A), bacterivorous (B), non-selective (N) and raptors (R). The trophic-functional structures of the ciliate communities showed significant variability among different water depths: (1) with increasing water depth, relative species numbers and relative abundances of groups A and R decreased sharply whereas those of groups B and N increased gradually; (2) in terms of the frequency of occurrences, group A dominated at depths of 1–3.5 m whereas group B dominated at 5 m, while in terms of the probability density function of the trophic-functional spectrum, group A was the highest contributor at 1 m and group B was highest at the other three depths; (3) distance-based redundancy analyses revealed significant differences in trophic-functional patterns among the four depths, except between 2 and 3.5 m (P > 0.05); and (4) the trophic-functional trait diversity increased from 1 to 3.5 m and decreased sharply at 5 m. Our results suggest that the biofilm-dwelling ciliates maintain a stable trophic-functional pattern and high biodiversity at depths of 1–3.5 m.     

Studies on ciliated protozoa in eutrophic lakes: 2. Field and laboratory studies on the effects of oxygen and other chemical gradients on ciliate distribution

An investigation into the spatial distribution of hypolimnetic ciliates in three small eutrophic lakes during the period of summer stratification was carried out. Peak ciliate densities were found to occur at the oxic/anoxic boundary, ciliate numbers declining with increasing depth within the hypolimnion. The ciliates only occurred in aerobic water where oxygen levels were less than about 0.5 mgl^–1 Laboratory experiments demonstrated that the ciliates swim upwards under anaerobic conditions but swim rapidly downwards under aerobic conditions. Further laboratory experiments showed that although the bulk of the population occured within anaerobic water, the hypolimnetic ciliates are aerobes and cannot survive indefinite anoxia. Despite the demonstrable toxicity of high levels of ammonia and sulphide, it was probably excesive distance from an available source of oxygen that excluded the ciliates from the lowest levels of the hypolimnion. Possible mechanisms which allowed these aerobic ciliates to colonise anaerobic water are considered.     

Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea

Subsurface microbial communities are generally thought to be structured through in situ environmental conditions such as the availability of electron acceptors and donors and porosity, but recent studies suggest that the vertical distribution of a subset of subseafloor microbial taxa, which were present at the time of deposition, were selected by the paleodepositional environment. However, additional highly resolved temporal records of subsurface microbiomes and paired paleoenvironmental reconstructions are needed to justify this claim. Here, we performed a highly resolved shotgun metagenomics survey to study the taxonomic and functional diversity of the subsurface microbiome in Holocene sediments underlying the permanently stratified and anoxic Black Sea. Obligate aerobic bacteria made the largest contribution to the observed shifts in microbial communities associated with known Holocene climate stages and transitions. This suggests that the aerobic fraction of the subseafloor microbiome was seeded from the water column and did not undergo post‐depositional selection. In contrast, obligate and facultative anaerobic bacteria showed the most significant response to the establishment of modern‐day environmental conditions 5.2 ka ago that led to a major shift in planktonic communities and in the type of sequestered organic matter available for microbial degradation. No significant shift in the subseafloor microbiome was observed as a result of environmental changes that occurred shortly after the marine reconnection, 9 ka ago. This supports the general view that the marine reconnection was a gradual process. We conclude that a high‐resolution analysis of downcore changes in the subseafloor microbiome can provide detailed insights into paleoenvironmental conditions and biogeochemical processes that occurred at the time of deposition.     

The symbiotic intestinal ciliates and the evolution of their hosts

The evolution of sophisticated differentiations of the gastro-intestinal tract enabled herbivorous mammals to digest dietary cellulose and hemicellulose with the aid of a complex anaerobic microbiota. Distinctive symbiotic ciliates, which are unique to this habitat, are the largest representatives of this microbial community. Analyses of a total of 484 different 18S rRNA genes show that extremely complex, but related ciliate communities can occur in the rumen of cattle, sheep, goats and red deer (301 sequences). The communities in the hindgut of equids (Equus caballus, Equus quagga), and elephants (Elephas maximus, Loxodonta africanus; 162 sequences), which are clearly distinct from the ruminant ciliate biota, exhibit a much higher diversity than anticipated on the basis of their morphology. All these ciliates from the gastro-intestinal tract constitute a monophyletic group, which consists of two major taxa, i.e. Vestibuliferida and Entodiniomorphida. The ciliates from the evolutionarily older hindgut fermenters exhibit a clustering that is specific for higher taxa of their hosts, as extant species of horse and zebra on the one hand, and Africa and Indian elephant on the other hand, share related ciliates. The evolutionary younger ruminants altogether share the various entodiniomorphs and the vestibuliferids from ruminants.     

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.     

Impairment of nucleoid segregation and cell division at high osmolarity in a strain of Escherichia coli overproducing the chaperone DnaK

Abstract Fourteen species of ciliates, seven of which are new, were found living in a sample of anoxic water collected from a small lake in Spain. The species belong to all six orders in which anaerobic ciliates have been described and they include the first anaerobic representatives of the order Prostomatida. This surprising diversity is probably sustained because it embraces all ciliate feeding types, and because protozoa are the only important consumers of the diversity of microbes in anoxic habitats. Six of the anaerobic ciliate species have aerobic congeners; this strengthens the contention that anaerobic ciliates evolved independently from aerobes belonging to several taxonomic groups.