An anaerobic protozoon, with symbiotic methanogens, living in municipal landfill material

Symbionts of Ciliates and Ciliates as Symbionts

Endosymbiotic relationships between ciliates and others are critical for their ecological roles, physiological adaptations, and evolutionary implications. These can be obligate and facultative. Symbionts often provide essential nutrients, contribute to the ciliate's metabolism, aid in digestion, and offer protection against predators or environmental stressors. In turn, ciliates provide a protected environment and resources for their symbionts, facilitating their survival and proliferation. Ultrastructural and full-cycle rRNA approaches are utilized to identify these endosymbionts. Fluorescence in situ hybridization using "species- and group-specific probes" which are complementary to the genetic material (DNA or RNA) of a particular species or group of interest represent convenient tools for their detection directly in the environment. A systematic survey of these endosymbionts has been conducted using both traditional and metagenomic approaches. Ciliophora and other protists have a wide range of prokaryotic symbionts, which may contain potentially pathogenic bacteria. Ciliates can establish symbiotic relationships with a variety of hosts also, ranging from protists to metazoans. Understanding ciliate symbiosis can provide useful insights into the complex relationships that drive microbial communities and ecosystems in general.

Spatial Distribution of Ciliate Assemblages in a Shallow Floodplain Lake with an Anaerobic Zone

The spatial distribution of ciliate assemblages was studied in a shallow floodplain lake with a sharp division of space by oxygen conditions. The surface zone occupied by the “carpet” of Lemna trisulca and L. minor was characterized by a large daily amplitude of oxygen content with periodic exceeding of 100% of saturation; the underlying water layer was characterized by microaerobic conditions throughout most of the year, with seasonal deviations towards oxygen-free conditions (in winter and mid-summer) or increased oxygen content (before freezing and after ice melt); stable oxygen-free conditions were maintained in the bottom layer of water and at the bottom of the lake. There were 111 species of ciliated protozoa recorded in the lake. The ciliated protozoa were clearly structured and formed three almost non-overlapping assemblages in terms of species composition, which retained their isolation during all seasons of the year. On the basis of the analysis performed using the R indicspecies package, species of ciliated protozoa were identified as indicators of conditions with different oxygen regimes, which are determined by the level of organic pollution and the distribution of photosynthetic organisms.

Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss

Hydrogenosomes are H2-producing mitochondrial homologs found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition, we generated genomic and transcriptomic data sets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.

Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge

Predation by protists is top-down pressure that regulates prokaryotic abundance, community function, structure, and diversity in natural and artificial ecosystems. Although the effects of predation by protists have been studied in aerobic ecosystems, they are poorly understood in anoxic environments. We herein studied the influence of predation by Metopus and Caenomorpha ciliates—ciliates frequently found in anoxic ecosystems—on prokaryotic community function, structure, and diversity. Metopus and Caenomorpha ciliates were cocultivated with prokaryotic assemblages (i.e., anaerobic granular sludge) in an up-flow anaerobic sludge blanket (UASB) reactor for 171 d. Predation by these ciliates increased the methanogenic activities of granular sludge, which constituted 155% of those found in a UASB reactor without the ciliates (i.e., control reactor). Sequencing of 16S rRNA gene amplicons using Illumina MiSeq revealed that the prokaryotic community in the UASB reactor with the ciliates was more diverse than that in the control reactor; 2,885–3,190 and 2,387–2,426 operational taxonomic units (>97% sequence similarities), respectively. The effects of predation by protists in anaerobic engineered systems have mostly been overlooked, and our results show that the influence of predation by protists needs to be examined and considered in the future for a better understanding of prokaryotic community structure and function.

Ciliates in extreme environments

As eukaryotic microbial life, ciliated protozoan may be found actively growing in some extreme condition where there is a sufficient energy source to sustain it because they are exceedingly adaptable and not notably less adaptable than the prokaryotes. However, a crucial problem in the study of ciliates in extreme environments is the lack of reliable cultivation techniques. To our knowledge, only a tiny fraction of ciliates can be cultured in the laboratory, even for a very limited period, which can partly explain the paucity of our understanding about ciliates diversity in various extremes although the interest in the biodiversity of extremophiles increased significantly during the past three decades. This mini-review aims to compile the knowledge of several groups of free-living ciliates that can be microscopically observed in extreme environmental samples, although most habitats have not been sufficiently well explored for sound generalizations.

Anaerobic ciliates from a sulphide-rich solution lake in Spain

We have examined and quantified the anaerobic ciliates living in the hypolimnion of a 14 m deep sulphide-rich (up to 0.73 mM) solution lake in Spain. At least seven ciliate species were found, numbering up to 50 ml-1 in total and reaching maximum abundance close to the sediment. Caenomorpha medusula, Lacrymaria elegans, L. sapropelica and Lagynus sp. were the most abundant species. Their vertical distributions were not related to the sulphide profile. Most ciliates were dependent on the sedimentation of cryptomonads, photosynthetic bacteria (especially Chromatium and Oscillatoria) and other bacteria from their sites of production in closely-juxtaposed mid-water plates. All anaerobic ciliates contained at least one type of symbiotic bacterium which showed methanogen autofluorescence. C. medusula, Lagynus sp. and Lacrymaria sapropelica also contained a large, non-fluorescing rod-shaped bacterium. In C. medusula, the methanogens and the non-fluorescing rods were both attached to the hydrogenosomes. In this ciliate alone, a third bacterial type was attached to the external ventral surface of the ciliate. Digestion of sulphide-oxidising bacteria by ciliates which harbour methanogenic bacteria provides a short bridge between the anaerobic sulphur and carbon cycles. Theoretical considerations of the rate of ciliate consumption of microbial carbon in the anoxic hypolimnion indicate that it is significant and that it may amount to 4 × 10(-5) g cm(-2)d(-1).

Cyclidium porcatum n. sp.: a Free-living anaerobic scuticociliate containing a stable complex of hydrogenosomes, eubacteria and archaeobacteria

A new ciliate species (Cyclidium porcatum) is the first freshwater anaerobic scuticociliate to be cultured and described. It contains a unique tripartite structure consisting of hydrogenosomes (confirmed by cytochemical staining for hydrogenase), interspersed with methanogens (confirmed by auto fluorescence and in situ hybridisation with an archaeobacterial 16S rRNA-specific probe) and unidentified eubacteria (confirmed with a eubacterial 16S rRNA-specific probe). This complex structure is stable and persistent, indicating that it is an anaerobic symbiotic consortium incorporating three functional partners.

Use of ciliates (Protozoa: Ciliophora) as bioindicator to assess sediment quality of two constructed mangrove sewage treatment belts in Southern China

To complement physical and chemical data, information of biological communities is important to assess the qualities of mangrove sediments receiving wastewater. Ciliate communities have cosmopolitan distribution, short life cycle and high sensitivity to pollutants, which make them useful as biological indicators of the sediment environment. In most literature, ciliates are widely used as bioindicators for the state of water quality. In this study, the physico-chemical parameters and ciliate community structure of surface sediment collected at different sampling points from two constructed mangrove (Aegiceras and Sonneratia) belts for treatment of municipal sewage in southern China were investigated. Results showed that most (> 80%) of the 216 species ciliates identified at the two constructed mangrove belts were either omnivorous or bacterivorous. Sediment redox potential (Eh) was considered an important factor to govern the distribution of ciliate species within the mangrove sediment. The saprobic system originally derived from freshwater ecosystem was used to evaluate the saprobic degrees of these constructed mangrove belts. Saprobic index (SI) values declined from the sewage inlet to the outlet points of the constructed belts, suggesting better sediment quality at the outlet point caused by treatment processes within the mangrove belt system. Sediment quality of the sewage outlet area of the constructed Aegiceras belt was determined as class II-III (SI = 2.48), while that of the Sonneratia belt was as class III (SI = 2.71) according to the saprobic classification, indicating that a better sewage treatment efficiency was apparent in the Aegiceras than Sonneratia belt. The present data suggested that ciliates could serve as a good bioindicator in assessing organically polluted sediment qualities.

Structural analysis of anaerobic granules in a phase separated reactor by electron microscopy

This paper discusses the microbial community structure of anaerobic granules and the effect of phase separation in anaerobic reactor on the characteristics of granules. Electron micrographs revealed that the core of anaerobic granular sludge consists predominantly of Methanosaeta-like cells, a key microorganism in granulation process. Granules in the methanogenic dominant zone of the reactor were stable and densely packed with smooth regular surface. On the other hand, granules subjected to acidogenic activities were less stable structures with broken parts and an irregular fissured surface. Anaerobic granules consisted of a vast diversity of species from the outer surface to the core of the granule and possessed a multi-layered structure. Viruses in the granules suggests the presence of bacteriophage in the granular biomass. These could be responsible for destroying cells and weakening the internal structure of granules, and thus possibly causing the breaking of granules. The observation of protozoa-like microorganism on the exterior zone of granular structure is believed to play an important role as bacterial predator and control the growth of bacterial cells. The images observed in this study shows that anaerobic granule harbour diverse number of microbial species, and act differently in acidogenic and methanogenic microbial zones.

Involvement of protozoa in anaerobic wastewater treatment process

It is only very rarely recognised in literature that anaerobic reactors may contain protozoa in addition to various bacterial and archeal groups. The role of protozoa in anaerobic degradation was studied in anaerobic continuous stirred tank reactors (CSTR) and batch tests. Anaerobic protozoa, especially the ciliated protozoa, have direct influence on the performance of CSTR at all organic loading rates (1-2g CODl(-1)d(-1)) and retention times (5-10 days). The studies revealed that chemical oxygen demand (COD) removal is strongly correlated to ciliate density in CSTR fed with oleate (suspended COD) and acetate (soluble COD). There was no significant difference in COD removal between reactors fed suspended COD and those fed soluble COD. However, the diversity and number of ciliates is greater in CSTR fed with particulate feed. The mixed liquor suspended solids (MLSS) representing biomass was significantly lower (16-34%) in CSTR with protozoa. In batch tests, increased COD removal and methane production was observed in sludge having ciliates as compared with sludge without protozoa. Methane production increased linearly with number of ciliates (R(2)=0.96) in batch tests with protozoa. Direct utilization of COD by flagellates and ciliates was observed in bacteria-suppressed cultures. The technological importance of these results is that reactors with protozoa-rich sludge can enhance the rate of mineralization of complex wastewater, especially wastewater containing particulate COD.

Methanogenic symbionts of anaerobic ciliates and their contribution to methanogenesis in an anoxic rice field soil

Methanogenesis in rice field soils starts soon after flooding while potentially competing processes like reduction of sulphate and iron take place. Early methanogenesis is mainly driven by hydrogen, while later in the season acetate tends to become more important. Anaerobic ciliates are abundant during this period, and their endosymbionts use hydrogen produced by the ciliates to reduce carbon dioxide to methane. These endosymbiotic methanogens are protected from the competition for substrates with other bacteria that may control methanogenesis outside the protozoan cells. Thus, we focussed on early methanogenesis and on the potential contribution from ciliates and their endosymbionts. Only ciliates of the genus Metopus were found to harbour methanogens, as identified by the F(420)-fluorescence of the endosymbionts. We followed the population dynamics of the ciliates with time, and calculated the ratio of symbiotic methane production to overall methanogenesis. Symbiotic methane production was calculated from the species-specific numbers of methanogenic endosymbionts times the cell-specific methane production of the symbionts. According to this calculation, the symbionts' contribution to overall methane production was only 6.4% at the beginning and decreased with time. In a second experiment, colchicine and cycloheximide were used to inhibit all eukaryotes, comparing the remaining methane production rate to a control without inhibitors. In the inhibition experiment, the contribution from symbionts decreased from 40% to 6% during the first days after flooding, and dropped to near zero within 2 weeks. However, nearly all methane produced from H(2)/CO(2) could be attributed to the ciliates' symbionts between days 5 and 10 after flooding. Both experiments showed that the contribution of methanogenic symbionts to overall methane production is a transient phenomenon, restricted to the first 2 weeks.

The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill

Inferred amino acid sequences of the methyl coenzyme-M reductase (mcrA) gene from five different methanogen species were aligned and two regions with a high degree of homology flanking a more variable region were identified. Analysis of the DNA sequences from the conserved regions yielded two degenerate sequences from which a forward primer, a 32-mer, and a reverse primer, a 23-mer, could be derived for use in the specific PCR-based detection of methanogens. The primers were successfully evaluated against 23 species of methanogen representing all five recognized orders of this group of Archaea, generating a PCR product between 464 and 491 bp. Comparisons between the mcrA and 16S small subunit rRNA gene sequences using PHYLIP demonstrated that the tree topologies were strikingly similar. Methods were developed to enable the analysis of methanogen populations in landfill using the mcrA gene as the target. Two landfill sites were examined and 63 clones from a site in Mucking, Essex, and 102 from a site in Odcombe, Somerset, were analysed. Analysis revealed a far greater diversity in the methanogen population within landfill material than has been seen previously.

Some rumen ciliates have endosymbiotic methanogens

Most of the small ciliate protozoa, including Dasytricha ruminantium and Entodinium spp. living in the rumen of sheep, were found to have intracellular bacteria. These bacteria were not present in digestive vacuoles. They showed characteristic coenzyme F420 autofluorescence and they were detected with a rhodamine-labelled Archaea-specific oligonucleotide probe. The measured volume percent of autofluorescing bacteria (1%) was close to the total volume of intracellular bacteria estimated from TEM stereology. Thus it is likely that all of the bacteria living in the cytoplasm of these ciliates were endosymbiotic methanogens, using H2 evolved by the host ciliate to form methane. Intracellular methanogens appear to be much more numerous than those attached to the external cell surface of ciliates.