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

Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa

Ciliated protozoa (ciliates) are unicellular eukaryotes, several of which are important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome of ciliates can promote a better understanding of the genetic mode and evolutionary history of these organisms and help optimize codons to improve gene editing efficiency in model ciliates. In this study, the following indices were calculated: the guanine-cytosine (GC) content, the frequency of the nucleotides at the third position of codons (T3, C3, A3, G3), the effective number of codons (ENc), GC content at the 3rd position of synonymous codons (GC3s), and the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, Neutrality plot analysis, ENc plot analysis, and correlation analysis were employed to explore the main influencing factors of CUB. The results showed that the GC content in the MAC genomes of each of 21 ciliate species, the genomes of which were relatively complete, was lower than 50%, and the base compositions of GC and GC3s were markedly distinct. Synonymous codon analysis revealed that the codons in most of the 21 ciliates ended with A or T and four codons were the general putative optimal codons. Collectively, our results indicated that most of the ciliates investigated preferred using the codons with anof AT-ending and that codon usage bias was affected by gene mutation and natural selection.

Molecular characterization of waterborne protozoa in surface water and sediment in Brazil: a taxonomic survey of ciliated protozoa and their correlation with Giardia duodenalis and Cryptosporidium spp

The detection of Giardia duodenalis and Cryptosporidium spp. was performed, along with the identification of the ciliated protozoa biodiversity, to evaluate the correlation between these protozoa in freshwater quality monitoring. Water and sediment samples from two sites in the Atibaia River (Campinas, São Paulo, Brazil) were collected monthly for 2 years (n = 96). Pathogenic protozoa in water and sediment were detected by using immunomagnetic separation, followed by visualization by immunofluorescence assay (IFA). All positive aliquots in IFA were subjected to DNA extraction and subsequently nested PCR. Qualitative (in vivo observation and silver impregnation) and quantitative (in vivo enumeration) analyses were performed for the ciliated protozoa. Giardia cysts were detected in 62.5% of the surface water samples and Cryptosporidium spp. in 25.0%. In the sediment, cysts were detected in 35.4% samples and oocysts in 16.6%. A total of 57 samples positive for Giardia cysts were subjected to sequencing, 40 of which were harboring G. duodenalis (24 were characterized as sub-assemblage AII). For ciliated protozoa, 73 taxa belonging to 53 genera were identified over the period of the study. These results revealed a high degree of contamination by waterborne protozoa in the main water source which supplies drinking water for more than one million people in Campinas (São Paulo), highlighting the need for continuous monitoring of this catchment site. In addition, the present study provides important data regarding the sources of the water body degradation, i.e., fecal contamination of human origin, in addition to the survey of the ciliated protozoa.

Sediment Microbiota as a Proxy of Environmental Health: Discovering Inter- and Intrakingdom Dynamics along the Eastern Mediterranean Continental Shelf

Sedimentary marine habitats are the largest ecosystem on our planet in terms of area. Marine sediment microbiota govern most of the benthic biological processes and therefore are responsible for much of the global biogeochemical activity. Sediment microbiota respond, even rapidly, to natural change in environmental conditions as well as disturbances of anthropogenic sources. The latter greatly impact the continental shelf. Characterization and monitoring of the sediment microbiota may serve as an important tool for assessing environmental health and indicate changes in the marine ecosystem. This study examined the suitability of marine sediment microbiota as a bioindicator for environmental health in the eastern Mediterranean Sea. Integration of information from Bacteria, Archaea, and Eukaryota enabled robust assessment of environmental factors controlling sediment microbiota composition: seafloor-depth (here representing sediment grain size and total organic carbon), core depth, and season (11%, 4.2%, and 2.5% of the variance, respectively). Furthermore, inter- and intrakingdom cooccurrence patterns indicate that ecological filtration as well as stochastic processes may control sediment microbiota assembly. The results show that the sediment microbiota was robust over 3 years of sampling, in terms of both representation of region (outside the model sites) and robustness of microbial markers. Furthermore, anthropogenic disturbance was reflected by significant transformations in sediment microbiota. We therefore propose sediment microbiota analysis as a sensitive approach to detect disturbances, which is applicable for long-term monitoring of marine environmental health. IMPORTANCE Analysis of data, curated over 3 years of sediment sampling, improves our understanding of microbiota assembly in marine sediment. Furthermore, we demonstrate the importance of cross-kingdom integration of information in the study of microbial community ecology. Finally, the urgent need to propose an applicable approach for environmental health monitoring is addressed here by establishment of sediment microbiota as a robust and sensitive model.

Protist Diversity Responses to Experimental N Deposition in Biological Crusts of a Semiarid Mediterranean Ecosystem

Biological soil crusts (BSC) are associations of different macro and microorganisms and aggregated soil particles located on the surface of soils in many different habitats. BSC harbour a diverse and complex community of ciliates and testate amoebae. These phagotrophic protists play an important role in C and N recycling in soil ecosystems but have not been frequently studied in BSC. In this context, the effects of three increasing N inputs on ciliates and testate amoebae in crusts from a semi-arid Mediterranean ecosystem were evaluated. A field experiment with artificial N-deposition was designed to mimic the effects caused by anthropogenic N depositions. The results have shown that the protist populations of these semi-arid Mediterranean environments have lower species richness than other soil environments. The increase in N produces a net loss of diversity in the populations studied and shifts in the community structure. It has also been shown that some ciliates and testate amoebae, due to their population responses to increased N concentrations, could potentially be used as bio-indicators of N contamination in these BSCs.

Does microplastic ingestion dramatically decrease the biomass of protozoa grazers? A case study on the marine ciliate Uronema marinum

Microplastic debris has become a significant global environmental issue. Yet, the effects on ingestion of microplastics by protozoan grazers-an important link in the microbial loop-are scant. Feeding experiments were conducted with the free-living marine ciliate Uronema marinum grazing on cultured bacteria Pseudoaltermonas sp., exposing them to different concentrations or sizes of polystyrene beads for 96 h. The number of beads decreased during exposure experiments. Under the microplastic influence, the ciliate cells were observed to decrease in abundance, body size, and biomass. It was noted that the ciliate biomass in the highest microplastic density treatment was significantly lower than that in the control (98.1% lower) and that microplastics can be ingested by ciliate protozoa which performed an important role in the transportation of energy across the microbial loop. Moreover, carbon biomass of ciliates exposed to microplastics of different particle diameters decreased significantly compared to the control. However, this effect does not seem to vary depending on microplastic sizes. This study is a first step in providing experimental insight into the feeding relationship between microplastics and marine protozoan grazers. Further research based on components of the microbial loop is needed to explore the impacts of microplastics in marine food webs.

Role of environmental factors in shaping the soil microbiome

The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.

High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient

Benthic macrofauna is regularly used in monitoring programmes, however the vast majority of benthic eukaryotic biodiversity lies mostly in microscopic organisms, such as meiofauna (invertebrates < 1 mm) and protists, that rapidly responds to environmental change. These communities have traditionally been hard to sample and handle in the laboratory, but DNA sequencing has made such work less time consuming. While DNA sequencing captures both alive and dead organisms, environmental RNA (eRNA) better targets living organisms or organisms of recent origin in the environment. Here, we assessed the biodiversity of three known bioindicator microeukaryote groups (nematodes, foraminifera, and ciliates) in sediment samples collected at seven coastal sites along an organic carbon (OC) gradient. We aimed to investigate if eRNA shotgun sequencing can be used to simultaneously detect differences in (i) biodiversity of multiple microeukaryotic communities; and (ii) functional feeding traits of nematodes. Results showed that biodiversity was lower for nematodes and foraminifera in high OC (6.2%-6.9%), when compared to low OC sediments (1.2%-2.8%). Dissimilarity in community composition increased for all three groups between Low OC and High OC, as well as the classified feeding type of nematode genera (with more nonselective deposit feeders in high OC sediment). High relative abundant genera included nematode Sabatieria and foraminifera Elphidium in high OC, and Cryptocaryon-like ciliates in low OC sediments. Considering that future sequencing technologies are likely to decrease in cost, the use of eRNA shotgun sequencing to assess biodiversity of benthic microeukaryotes could be a powerful tool in recurring monitoring programmes.

Towards an ecological understanding of the killer trait - A reproducible protocol for testing its impact on freshwater ciliates

Paramecium strains with the ability to kill other paramecia often harbour intracellular bacteria belonging to the genera Caedibacter or Caedimonas. Central structures of this killer trait are refractile bodies (R-bodies) produced by the endosymbionts. Once ingested by a sensitive Paramecium, R-bodies presumably act as delivery system for an unidentified toxin which causes the death of endosymbiont-free paramecia while those infected gain resistance from their symbionts. The killer trait is therefore considered as competitive advantage for the hosts of R-body producers. While its effectiveness against paramecia is well documented, the effects on other aquatic ciliates are much less studied. In order to address the broadness of the killer trait, a reproducible killer test assay considering the effects on predatory ciliates (Climacostomum virens and Dileptus jonesi) as well as potential bacterivorous Paramecium competitors (Dexiostoma campyla, Euplotes aediculatus, Euplotes woodruffi, and Spirostomum teres) as possibly susceptible species was established. All used organisms were molecularly characterized to increase traceability and reproducibility. The absence of any lethal effects in both predators and competitors after exposure to killer paramecia strongly suggests a narrow action range for the killer trait. Thus, R-body producing bacteria provide their host with a complex, costly strategy to outcompete symbiont-free congeners only.

Environmental status assessment using biological traits analyses and functional diversity indices of benthic ciliate communities

In this study, we tested the hypothesis that the functional diversity of benthic ciliates has high potential to monitor marine ecological status. Therefore, we investigated the spatial and temporal variation of functional diversity of benthic ciliates in the Yangtze Estuary during one year using biological traits analyses and functional diversity indices. Traits and community compositions showed clear spatial and temporal variations. Among a variety of biological traits, feeding type and body size emerged as strongest predictable variables. Functional divergence (FDiv) had an advantage over two other functional diversity indices, as well as over classical diversity measures (i.e. richness, evenness, Shannon-Wiener) to infer environmental status. Significant correlations between biological traits, FDiv and environmental variables (i.e. nutrients, temperature, salinity) suggested that functional diversity of benthic ciliates might be used as a bio-indicator in environmental status assessments. Further mandatory researches need to implement functional diversity of ciliates in routine monitoring programs were discussed.

Cilioprotists as biological indicators for estimating the efficiency of using Gravel Bed Hydroponics System in domestic wastewater treatment

Interest has increased over the last several years in using different methods for treating sewage. The rapid population growth in developing countries (Egypt, for example, with a population of more than 87 millions) has created significant sewage disposal problems. There is therefore a growing need for sewage treatment solutions with low energy requirements and using indigenous materials and skills. Gravel Bed Hydroponics (GBH) as a constructed wetland system for sewage treatment has been proved effective for sewage treatment in several Egyptian villages. The system provided an excellent environment for a wide range of species of ciliates (23 species) and these organisms were potentially very useful as biological indicators for various saprobic conditions. Moreover, the ciliates provided excellent means for estimating the efficiency of the system for sewage purification. Results affirmed the ability of this system to produce high quality effluent with sufficient microbial reduction to enable the production of irrigation quality water.

Are ciliated protozoa communities affected by macrophyte species, date of sampling and location in horizontal sub-surface flow constructed wetlands?

The effects of design and operational factors on the dynamics of ciliated protozoa in constructed wetlands (CWs) treating wastewater remain poorly known, although bacterivory by ciliates could have important implications for nutrient cycling in these systems. We conducted a greenhouse experiment with eight wetland mesocosms (1 m(2)) fed with synthetic wastewater to assess how macrophyte species (Phragmites australis, Phalaris arundinacea, and Typha angustifolia), location within CW (longitudinal, depth), and temporal fluctuations affect ciliate abundance and diversity. Urosoma similis was the most abundant taxon, but Hypotrichidae, Scuticociliates, Drepomonas revoluta, and Acineria uncinata were also abundant. Longitudinal location had the highest impact on ciliate dynamics, with more abundant and diverse communities in the initial section of wetlands. P. australis/T. angustifolia and P. arundinacea had the most and least favorable conditions for ciliates, respectively, but differences among macrophytes were mostly not significant. Ciliate abundance appeared to decline from August to November, most likely because of lower temperature and plant inputs of organic matter and oxygen. Depth had no apparent impact on ciliate dynamics, suggesting that sampling at multiple depths in CW is not necessary to adequately monitor ciliate communities. Overall, our results suggest that macrophytes, location, and date of sampling influenced ciliated dynamics but stress the need for direct manipulative experiments of ciliate abundance, diversity, and composition conducted on a full annual cycle to better understand the impact of ciliates on nutrient cycling in CWs. This is especially true to determine if the associations found in our principal component analysis are robust.

An approach to analyzing spatial patterns of protozoan communities for assessing water quality in the Hangzhou section of Jing-Hang Grand Canal in China

INTRODUCTION

In order to evaluate water quality of a canal system, the spatial pattern of protozoan communities in response to physicochemical variables was studied in the Hangzhou section of the Grand Canal, northern China during a 1-year cycle (February 2008-January 2009).

MATERIALS AND METHODS

Protozoan samples were monthly collected at six sampling stations with a spatial gradient of environmental status. Physicochemical parameters, e.g., water temperature, dissolved oxygen, chemical oxygen demand (COD), biological oxygen demand, total nitrogen (TN), and total phosphorus (TP), were measured synchronously for comparison with biotic parameters.

RESULTS

The protozoan community structures represented significant differences among the six sampling stations. The spatial patterns of protozoan communities were significantly correlated with the changes of chemical variables, especially COD, either alone or in combination with TP and/or TN. Of 88 protozoan taxa recorded over the study period, ten species (e.g., Carchesium polypinum, Colpidium campylum, Prorodon teres, Vorticella putrina, Zoothamnium arbuscula, Euglena spp., and Phacus spp.) were significantly related to COD, either alone or in combination with TP and/or TN.

CONCLUSION

These findings suggest that protozoa can be used as a robust bioindicator of water quality in freshwater river systems.