Morphology and molecular phylogeny of three Parasonderia species including a new species (Ciliophora, Plagiopylea)

Ciliates of the class Plagiopylea play a vital role in various anaerobic environments as consumers of prokaryotes. Yet, the diversity and phylogeny of this group of ciliates, especially marine representatives, remain poorly known. In this study, three Parasonderia species, viz., Parasonderia elongata spec. nov., and the already known P. cyclostoma and P. vestita, discovered in anaerobic sediments from various intertidal zones in China, were investigated based on their living morphology, infraciliature, and small subunit ribosomal rRNA gene sequences. Parasonderia elongata can be recognized by its larger body size, elongated body shape, oval oral opening, number of oral kineties, and significantly shortened leftmost postbuccal polykineties on the cell surface. Improved diagnosis and redescription of P. cyclostoma is provided for the first time, including data on infraciliature and molecular sequence. Phylogenetic analyses revealed that the three species cluster together and with the sequence of a Chinese population of P. vestita already present in the GenBank database, forming a robust clade.

Group-specific functional patterns of mitochondrion-related organelles shed light on their multiple transitions from mitochondria in ciliated protists

Adaptations of ciliates to hypoxic environments have arisen independently several times. Studies on mitochondrion-related organelle (MRO) metabolisms from distinct anaerobic ciliate groups provide evidence for understanding the transitions from mitochondria to MROs within eukaryotes. To deepen our knowledge about the evolutionary patterns of ciliate anaerobiosis, mass-culture and single-cell transcriptomes of two anaerobic species, Metopus laminarius (class Armophorea) and Plagiopyla cf. narasimhamurtii (class Plagiopylea), were sequenced and their MRO metabolic maps were compared. In addition, we carried out comparisons using publicly available predicted MRO proteomes from other ciliate classes (i.e., Armophorea, Litostomatea, Muranotrichea, Oligohymenophorea, Parablepharismea and Plagiopylea). We found that single-cell transcriptomes were similarly comparable to their mass-culture counterparts in predicting MRO metabolic pathways of ciliates. The patterns of the components of the MRO metabolic pathways might be divergent among anaerobic ciliates, even among closely related species. Notably, our findings indicate the existence of group-specific functional relics of electron transport chains (ETCs). Detailed group-specific ETC functional patterns are as follows: full oxidative phosphorylation in Oligohymenophorea and Muranotrichea; only electron-transfer machinery in Armophorea; either of these functional types in Parablepharismea; and ETC functional absence in Litostomatea and Plagiopylea. These findings suggest that adaptation of ciliates to anaerobic conditions is group-specific and has occurred multiple times. Our results also show the potential and the limitations of detecting ciliate MRO proteins using single-cell transcriptomes and improve the understanding of the multiple transitions from mitochondria to MROs within ciliates.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00147-w.

Improved Methods for Bulk Cultivation and Fixation of Loxodes Ciliates for Fluorescence Microscopy

Loxodes is one of the best ecologically characterized ciliate genera with numerous intriguing physiological abilities, including gravity-sensing organelles and nitrate respiration. However, these cells have been considered challenging to cultivate in bulk, and are poorly preserved by conventional fixatives used for fluorescence microscopy. Here we describe methods to grow and harvest Loxodes cells in bulk with liquid soil extract medium, as well as a new fixative called ZFAE (zinc sulfate, formaldehyde, acetic acid, ethanol) that can fix Loxodes cells more effectively than buffered formaldehyde or methanol. We show that ZFAE is compatible with immunofluorescence and the nuclear stain DAPI. Loxodes is thus now amenable to long-term maintenance, large-scale growth, and modern cell biology investigations of monoclonal strains in laboratory conditions.

Anaerobic Ciliates as a Model Group for Studying Symbioses in Oxygen-depleted Environments

Anaerobiosis has independently evolved in multiple lineages of ciliates, allowing them to colonize a variety of anoxic and oxygen-depleted habitats. Anaerobic ciliates commonly form symbiotic relationships with various prokaryotes, including methanogenic archaea and members of several bacterial groups. The hypothesized functions of these ecto- and endosymbionts include the symbiont utilizing the ciliate's fermentative end-products to increase host's anaerobic metabolic efficiency, or the symbiont directly providing the host with energy by denitrification or photosynthesis. The host, in turn, may protect the symbiont from competition, the environment, and predation. Despite rapid advances in sampling, molecular, and microscopy methods, as well as the associated broadening of the known diversity of anaerobic ciliates, many aspects of these ciliate symbioses, including host-specificity and co-evolution, remain largely unexplored. Nevertheless, with the number of comparative genomic and transcriptomic analyses targeting anaerobic ciliates and their symbionts on the rise, insights into the nature of these symbioses and the evolution of the ciliate transition to obligate anaerobiosis continue to deepen. This review summarizes the current body of knowledge regarding the complex nature of symbioses in anaerobic ciliates, the diversity of these symbionts, their role in the evolution of ciliate anaerobiosis and their significance in ecosystem-level processes.

Evolutionary insights and brief review of Loxodes Ehrenberg, 1830 (Ciliophora, Karyorelictea, Loxodidae) with description of a new species from Mexico

Karyorelictids are a group of ciliates inhabiting marine and freshwater biotopes and possessing a non-dividing macronucleus. We describe a new freshwater species based on morphology and the 18S rRNA gene sequence data. Loxodes tziscaensis n. sp. can be easily distinguished from other Loxodes species by the arrangement of the nuclear apparatus and features of the buccal and somatic ciliature. The current proposed 18S rRNA phylogeny of Loxodes, including seven Loxodes species, shows two morphologically well-supported groups. Group A (L. rostrum, type species; L. vorax and L. tziscaensis n. sp.) includes species with a single nuclear group (two macronuclei and one micronucleus), in contrast to species of group B, which possess more than one nuclear group (L. striatus, L. magnus, L. kahli, L. penardi, and L. rex). We propose that the last common ancestor of Loxodes was a marine Remanella-like species possessing a single nuclear group. The division and differentiation of the micronucleus into a new macronucleus and the retention of the old macronuclei, independently of cell division, may have been two crucial processes during the evolution and diversification of Loxodes species with one nuclear group into species with multiple nuclear groups.

Spatial variation in ciliate communities with respect to water quality in the Delhi NCR stretch of River Yamuna, India

The River Yamuna emerges from Saptarishi Kund, Yamunotri and merge with River Ganges at Allahabad, India. Anthropogenic stress has affected the water quality of the river Yamuna drastically in the stretch traversing Delhi and its satellite towns (National Capital Region, NCR). In the present study, effect of water quality on the microbial life in the River Yamuna was analyzed using ciliate communities (Protista, Ciliophora) as bio-indicators. Water samples were collected from six sampling sites chosen according to the levels of pollution along the river and water quality was analysed using standard physicochemical factors. As the river traverses Delhi NCR, water quality deteriorates considerably as indicated by the Water Quality Index at the selected sampling sites. Seventy-four ciliate species representing nine classes were recorded. Based on the Shannon diversity index, maximum species diversity was found at the point where the river enters Delhi. The saprobity index showed the river water was beta-mesosaprobic when the river enters Delhi and alpha-mesosaprobic at downstream sites after the first major drain outfall. Significant relationship between the spatial variation in ciliate communities and abiotic parameters indicate that ciliates can be used as effective bioindicators of pollution in the River Yamuna.

Response of Anaerobic Protozoa to Oxygen Tension in Anaerobic System

The effect of oxygen on anaerobic protozoa was studied in anaerobic batch reactors inoculated with sludge and protozoa cultures. Among the protozoa genera, Metopus, Brachonella, Plagiopyla, Trepomonas, and Vanella were more sensitive to oxygen compared to other genera. Protozoa genera Menoidium, Rhynchomonas, Cyclidium, Spathidium, and Amoeba were found to survive under aerobic conditions, and the growth rate was slightly higher or similar to anaerobic condition. O₂ tension resulted in the loss of free and endosymbiotic methanogens in anaerobic system, while methanogens were observed inside the protozoan cysts. Survival of anaerobic protozoa declined considerably when the O₂ tension exceeded 1% atm. sat. and showed chemosensory behavior in response to O₂ exposure. Superoxide dismutase activity was detected in survived protozoa cells under O₂ tension. Facultative anaerobic protozoa with SOD activity can provide a mechanism to overcome possible occurrence of oxygen toxicity in the treatment of wastewater in anaerobic reactor.

Unusual features of non-dividing somatic macronuclei in the ciliate class Karyorelictea

Genome structure and nuclear organization have been intensely studied in model ciliates such as Tetrahymena and Paramecium, yet few studies have focused on nuclear features of other ciliate clades including the class Karyorelictea. In most ciliates, both the somatic macronuclei and germline micronuclei divide during cell division and macronuclear development only occurs after conjugation. However, the macronuclei of Karyorelictea are non-dividing (i.e. division minus (Div-)) and develop anew from micronuclei during each asexual division. As macronuclei age within Karyorelictea, they undergo changes in morphology and DNA content until they are eventually degraded and replaced by newly developed macronuclei. No less than two macronuclei and one micronucleus are present in karyorelictid species, which suggests that a mature macronucleus 1) might be needed to sustain the cell while a new macronucleus is developing and 2) likely plays a role in guiding the development of the new macronucleus. Here we use a phylogenetic framework to compile information on the morphology and development of nuclei in Karyorelictea, largely relying on the work of Dr. Igor Raikov (1932-1998). We synthesize data to speculate on the functional implications of key features of Karyorelictea including the presence of at least two macronuclei in each cell and the inability for macronuclei to divide.

Morphology and phylogeny of two species of Loxodes (Ciliophora, Karyorelictea), with description of a new subspecies, Loxodes striatus orientalis subsp. n

The morphology and phylogeny of Loxodes vorax and L. striatus orientalis subsp. n. were investigated based on infraciliature and small subunit (SSU) rRNA gene sequence data. Loxodes striatus orientalis subsp. n. was separated from L. striatus striatus stat. n. by having fewer dikinetids in the intrabuccal kinety (35-55 vs. 50-70) and a variable number of macronuclei (2-4 vs. 2). In addition, the SSU rRNA gene sequence of the new subspecies differs in 13 and 11 nucleotides from that of two populations of the nominotypic subspecies. We also summarized the morphological differences between Loxodes and Remanella based on the data available. Phylogenetic analyses revealed that the genus Loxodes was monophyletic and nested within Remanella species. This study might, therefore, support the hypothesis that the freshwater genus Loxodes evolved from the marine genus Remanella.

Oxygen tolerance and occurrence of superoxide dismutase as an antioxidant enzyme in Metopus es

The free-living anaerobic ciliate Metopus es was found to possess moderate tolerance to oxygen. Direct oxygen exposure led to the death of >80% of the population within 24h, but the remaining cells exhibited some oxygen tolerance and survived up to 4 days without any growth. Survival of the ciliate was observed only in an oxygen tension up to 7.0microM, and higher O(2) concentrations (>7.0microM) were found to be detrimental with a K(m) value of 3.5microM. The percentage of survival (50%) was higher when the culture was exposed to a low oxygen level (1.3microM) and it decreased with increasing oxygen tension. No catalase activity was detected in the extract of surviving ciliates. Maximum superoxide dismutase (SOD) activity of 1.52+/-0.4U/mg protein was observed at 1.3microM oxygen. SOD activity was not affected by cyanide or hydrogen peroxide, indicating that it belongs to the Mn type of SOD. Methanogenic endosymbionts in M. es lost their autofluorescence on oxygen exposure of >5.0microM, but their viability was not permanently affected, as indicated by the maintenance of a similar number of methanogens/cell upon restoring the anaerobic condition.

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.

Graviresponses of gliding and swimming Loxodes using step transition to weightlessness

Cells of Loxodes striatus were adjusted to defined culturing, experimental solution O2-supply, temperature, and state of equilibration to be subjected to step type transition of acceleration from normal gravity, (1 g) to the weightless condition (microgravity) during free fall in a 500 m drop shaft. Cellular locomotion inside a vertical experimental chamber was recorded preceding transition and during 10 s of microgravity. Cell tracks from video records were used to separate cells gliding along a solid surface from free swimmers, and to determine gravitaxis and gravikenesis of gliding and swimming cells. With O2 concentrations > or = 40% air saturation gliders and swimmers showed a positive gravitaxis. In microgravity gravitaxis of gliders relaxed within 5 s whereas gravitaxis relaxation of swimmers was not completed even after 10 s. Rates of horizontal gliders (319 micrometers/s) exceeded those, of horizontal swimmers (275 micrometers/s). Relaxation of gravikinesis was incomplete after 10 s of microgravity. Analysis of the locomotion rates during the g-step transition revealed that gliders sediment more slowly, than swimmers (14 versus 45 micrometers/s). The gravikinesis of gliders cancelled sedimentation effects during upward and downward locomotion tending to maintain cells at a predetermined level inside sediments of a freshwater habitat. At > or = 40% air saturation, gravikinesis of swimmers augmented the speed of the majority of cells during gravitaxis, which favours fast vertical migrations of Loxodes.

The role of ciliated protozoa in pelagic freshwater ecosystems

The abundance and biomass of ciliates are both strongly related to lake trophic status as measured by chlorophylla concentrations. Taxonomic replacements occur with increasing eutrophication such that large-bodied forms (predominantly oligotrichs) are progressively replaced by smaller-bodied ciliates (mainly scuticociliates). Highly acidic lakes display a more pronounced dominance of large-bodied forms when contrasted with less acidic lakes of comparable trophy. Community structure of ciliate populations is determined largely by lake trophy with acidic oligotrophic systems being characterized by reduced diversity and species richness compared with hypereutrophic systems. The temporal and spatial distribution of small (< 100μm) ciliate populations is ascribed to lake thermal regimes which provide localized concentrations of food resources. Likewise, in extremely productive lakes, very large (> 100μm) meroplanktonic ciliates enter the water column during midsummer after the development of thermal stratification and associated profundal deoxygenation. Laboratory studies indicate that large zooplankton (crustaceans) are capable of utilizing ciliates as a food source, but there is little direct evidence from field studies documenting this trophic link. Ciliates can be voracious grazers of both bacterioplankton and phytoplankton, and each species has a distinct range of preferred particle size which is a function of both mouth size and morphology. Myxotrophic ciliates may be important components in some plankton communities, particularly during periods of nutrient limitation or after their displacement from the benthos of eutrophic lakes. Evidence regarding the importance of planktonic ciliated protozoa in nutrient regeneration and as intermediaries in energy flow is discussed.