Report and Phylogeny of a Novel Euplotes Species from China:E.mazeii n.sp.,and Review of E.balteatus(Alveolata,Ciliophora)

The freshwater species,Euplotes mazeii n.sp.,and the marine species,E.balteatus(Dujardin,1841)Diesing,1850 were collected from China and investigated based on their living morphology,ciliary pattern,and small subunit ribosomal RNA(SSU rRNA)gene sequence data.Euplotes mazeii n.sp.was characterized by its small cell size((40-55)μm×(25-35)μm),nine frontoventral cirri,one marginal and two caudal cirri,seven dorsal kineties,and a double-eurystomus type of dorsal silverline system.Phylogenetic analyses based on molecular data confirmed the branching position of this new taxa within the genus Euplotes,with 5.01%(84 nucleotides)sequence variation,supporting the identification of a new species.We re-examined all described and supposedly conspecific populations and give a review of Euplotes balteatus.E.balteatus has been reported frequently;however,E.balteatus sensu Agamaliev,1968 is different from other populations in the number of marginal cirri or the type of silverline system,which suggests there might be a misidentification.The SSU rRNA gene sequences of two populations of E.balteatus from the studies of Chen et al.(2013)and Pan et al.(2012)differ from each other by more than 135 nucleotides,implying that the identity of the species currently associated with the SSU rRNA gene sequence in molecular databases requires further confirmation.

Morphology and Molecular Phylogeny of Two Marine Folliculinid Ciliates Found in China (Ciliophora, Heterotrichea)

Ciliates of the heterotrich family Folliculinidae are characterized by their transparent lorica,conspicuous peristomial lobes pair and dimorphic life cycle,a sessile trophont and a motile swarmer.However,understanding their biodiversity and systematics is relatively poor.In the present study,two species representing two genera of folliculinids,which were collected from marine and brackish habitats in China,were investigated with morphological and molecular methods.The genus Diafolliculina n.gen.is established for D.longilobata n.sp.Detailed morphological redescriptions for another species Eufolliculina is provided.Moreover,phylogenetic analysis based on small subunit ribosomal DNA(SSU rDNA)sequences showed that 1)all two genera locate in the Folliculinidae clade;2)Metafolliculina clusters with Eufolliculina;and 3)two genera(Diafolliculina and Ampullofolliculina)with a lorica closure device have close affinities with Folliculina.The lorica of Diafolliculina and Ampullofolliculina lacks a closure device,thereby the phylogeney contradicts the morphology-based classification.

An efficient method for constructing a random insertional mutant library for forward genetics in Nannochloropsis oceanica

Insertional mutation,phenotypic evaluation,and mutated gene cloning are widely used to clone genes from scratch.Exogenous genes can be integrated into the genome during non-homologous end joining(NHEJ)of the double-strand breaks of DNA,causing insertional mutation.The random insertional mutant library constructed using this method has become a method of forward genetics for gene cloning.However,the establishment of a random insertional mutant library requires a high transformation efficiency of exogenous genes.Many microalgal species show a low transformation efficiency,making constructing random insertional mutant libraries difficult.In this study,we established a highly efficient transformation method for constructing a random insertional mutant library of Nannochloropsis oceanica,and tentatively tried to isolate its genes to prove the feasibility of the method.A gene that may control the growth rate and cell size was identified.This method will facilitate the genetic studies of N.oceanica,which should also be a reference for other microalgal species.

Domestication of marine microalga Nannochloropsis oceanica to freshwater medium and the physiological responses

Marine microalga Nannochloropsis oceanica LAMB0001 were domesticated (~730 generations,~two days each) to adapt freshwater BG11 medium. A number of freshwater medium adapted colony-derived strains were obtained. The strains were verified phylogenetically to be N. oceanica LAMB0001 based on the 18S ribosomal RNA gene. Freshwater-medium adapted strain (FA1) grew faster in the BG11 medium prepared with freshwater than wild-type N. oceanica grew in f/2 medium prepared with seawater. We assumed that (1) the expression patterns of the genes that expressed differentially between FA1 and the wild-type N. oceanica exposing to the BG11 medium (WT-F) have been reprogrammed;(2) the physiological processes in which these genes involved have been modified;and (3) a Gene Ontology (GO) term or a KEGG pathway enriched by DEGs between FA1 and WT-F has been up- or down-regulated if it was enriched simultaneously by up- or down-regulated DEGs between FA1 and WT-F, respectively. Under these assumptions, we found that FA1 reprogrammed the expression patterns of a set of genes that involved in cell adhesion, membrane and membrane integrity, material transportation, cell movement, and cellular signaling network. These changes in cellular functions and metabolic pathways indicate that the microalga modified its gene expression pattern in a wide function range and at a high regulation rank in order to adapt to the freshwater medium. It is feasible to domesticate marine microalgae to a freshwater habitat, which may aid to modify their cultivation performances.

A new record of a flathead fish (Teleostei: Platycephalidae) from China based on morphological characters and DNA barcoding

A new record of Platycephalus sp.1 （sensu Nakabo, 2002） was documented based on morphological characters and DNA barcoding. We collected 174 specimens of the genus Platycephalus from Chinese coastal waters of Dongying, Qingdao, Zhoushan, and Beihai. Samples were identified as Platycephalus sp. 1 morphologically. The coloration, meristic traits, and morphometric measurements are consistent with previously published records. In brief, it is an orange-brown flathead fish with dark brown spots scattered on head and body, lateral line scales 83 to 99 with one or two spine-bearing anteriormost pored scale, no yellow blotch on the caudal fin. Cytochrome oxidase I subunit （COI） gene fragments were sequenced for phylogenetic analysis. The mean evolutionary distance within the species Platycephalus sp. 1 was 0.1%. Net evolutionary distances between Platycephalus sp. 1 and other species of Platycephalus ranged from 10.8% to 19.7%, which is much greater than the threshold for species delimitation. The COl sequence analysis strongly supports the validity ofPlatyceohalus sp. 1 at genetic level.

Improvement of Nannochloropsis oceanica growth performance through chemical mutation and characterization of fast growth physiology by transcriptome profiling

Nannochloropsis oceanica promises to be an industrial-level producer of polyunsaturated fatty acids. In this study, the fastest and slowest growing N. oceanica mutants were selected through N-methyl-N＇-nitro-N-nitrosoguanidine mutation, and two mutant strains and the wild type （WT） subjected to transcriptome profiling. It was found that the 0D680 reads at stationary growth phase of both WT and its mutants were proportional to their cell density, thus indicating their division rate and growth speed during culture. This chemical mutation was effective for improving growth performance, and the fast strain divided faster by upregulating the expression of genes functioning in the cell cycle and downregulating genes involved in synthesis of amino acids, fatty acids, and sugars as well as the construction of ribosome and photosynthetic machinery. However, the relationship among the effected genes responsible for cell cycle, metabolism of fatty and amino acids, and construction of ribosome and photosynthetic machinery remained unclear. Further genetic studies are required for clarifying the genetic/metabolic networks underpinning the growth performance ofN. oceanica. These findings demonstrated that this mutation strategy was effective for improving the growth performance of this species and explored a means ofmicroalgal genetic improvement, particularly in species possessing a monoploid nucleus and asexual reproduction.

A new record of Sebastes koreanus from China based on morphological characters and DNA barcoding

A new record of Sebastes koreanus （Kim and Lee, 1994） was documented based on morphological characters and DNA barcoding. Fifty-six Sebastes specimens were collected from the coastal waters of northern China. Samples were identified as S. koreanus based on morphological characters. The coloration and morphometric measurements were consistent with those described from specimens collected in South Korea. In this study, specimens had the following morphological characteristics： light brown body with dark stripes and tiny dark spots, 4-5 wide indistinct vertical patterns on the side, 2 radial stripes behind and below the eyes, 1 large dark blotch on the opercle. Additionally, the following meristie characters were recorded： dorsal fin XIV-13, pectoral fin 16, anal fin III-6-7, pelvic fin [-5, lateral line scales 29-30, and vertebrae 26. The fragment of cytochrome oxidase subunit I （CO1） gene of mitochondrial DNA was sequenced for phylogenetic analysis. The mean genetic distance within the species was 0.3%. Net genetic distances between S. koreanus and other Sebastes species ranged from 3.1% to 7.6%, which was greater than the threshold for species delimitation. The phylogenetic analysis strongly supports the validity of S. koreanus in China at the genetic level. The origion, evolution, patterns of speciation and unique features in genome divergence among primate lineages of this species still need future directions of research.

Molecular phylogeny and species separation of five morphologically similar Holosticha-complex ciliates(Protozoa, Ciliophora) using ARDRA riboprinting and multigene sequence data

To separate and redefine the ambiguous Holosticha-complex, a confusing group of hypotrichous ciliates, six strains belonging to five morphospecies of three genera, Holosticha heterofoissneri, Anteholosticha sp. popl, Anteholosticha sp. pop2, A. manca, A. gracilis and Nothoholostichafasciola, were analyzed using 12 restriction enzymes on the basis of amplified ribosomal DNA restriction analysis. Nine of the 12 enzymes could digest the DNA products, four （HinfⅠ, Hind Ⅲ, Msp Ⅰ, Taq Ⅰ） yielded species-specific restriction patterns, and Hind Ⅲ and Taq Ⅰ produced different pattems for two Anteholosticha sp. populations. Distinctly different restriction digestion haplotypes and similarity indices can be used to separate the species. The secondary structures of the five species were predicted based on the ITS2 transcripts and there were several minor differences among species, while two Anteholosticha sp. populations were identical. In addition, phylogenies based on the SSrRNA gene sequences were reconstructed using multiple algorithms, which grouped them generally into four clades, and exhibited that the genus Anteholosticha should be a convergent assemblage. The fact that Holosticha species clustered with the oligotrichs and choreotrichs, though with very low support values, indicated that the topology may be very divergent and unreliable when the number of sequence data used in the analyses is too low.

Population dynamics of marine ciliate Euplotes vannus (Protozoa, Ciliophora) in different artificial seawaters

To study population dynamics of marine ciliates in different artificial seawaters （ASW）, the population growth dynamics of a common marine ciliate Euplotes vannus were investigated using beef extract media and rice media for five types of ASW and natural seawater （NSW）. The results show that： （1） the population growth rate was in the order of NSW〉Flack ASW〉Nakamula ASW〉Schmadz ASW〉Oshima ASW〉Subow ASW and was considerably higher in rice media than in beef extract media （apart from Subow ASW）; （2） the maximum density of E. vannus in stationary phase in each treatment was ranked as Hack ASW〉Nakamula ASW〉Schmadz ASW〉NSW〉Oshima ASW〉Subow ASW, and was again higher in rice media than in beef extract media （except for Subow ASW）; （3） the exponential and stationary phases were longer in rice media than in beef extract media; （4） strains of E. vannus that had been domesticated for 〉1 year in ASW grew significantly slower, with lower maximum density and longer stationary phase than those isolated and maintained in NSW. It was demonstrated that： （1） E. vannus may grow well in Flack, Nakamula and Schmads ASW compared with NSW （mainly in terms of growth rate）; and （2） Oshima ASW is the preferred choice for stock cultures of E. vannus, but the ASWs Flack, Nakamula and Schmadz are preferred for mass culture. These findings suggest that these three ASWs are effective for the cultivation of marine protozoa for experimental studies on ecology, toxicology and molecular biology.

Structure of Mitochondrial DNA Control Region of Pholis fangi and Its Phylogenetic Implication

In this study, the entire mitochondrial DNA(mtDNA) control region(CR) of Pholis fangi was amplified via polymerase chain reaction followed by direct sequencing. The length of the mtDNA CR consensus sequence of P. fangi was 853 bp in length. In accordance with the recognition sites as were previously reported in fish species, the mtDNA CR sequence of P. fangi can be divided into 3 domains, i.e., the extended terminal associated sequence(ETAS), the central conserved sequence block(CSB), and the CSB domain. In addition, the following structures were identified in the mtDNA CR sequence of P. fangi: 2 ETASs in the ETAS domain(TAS and cTAS), 6 CSBs in the central CSB domain(CSB-F to CSB-A), and 3 CSBs in the CSB domain(CSB-1 to CSB-3). These demonstrated that the structure of the mtDNA CR of P. fangi was substantially different from those of most other fish species. The mtDNA CR sequence of P. fangi contained one conserved region from 656 bp to 815 bp. Similar to most other fish species, P. fangi has no tandem repeat sequences in its mtDNA CR sequence. Phylogenetic analysis based on the complete mtDNA CR sequences showed that there were no genetic differences within P. fangi populations of the same geographical origin and between P. fangi populations of different geographical origins.

Morphological characters and DNA barcoding of Syngnathus schlegeli in the coastal waters of China

A Syngnathus species widely distributed in Chinese seas was permanently identified as Syngnathus acus by native ichthyologists, but the taxonomic description about this species was inadequate and lacking conclusively molecular evidence. To identify this species, 357 individuals of this species from the coastal waters of Dandong, Yantai, Qingdao and Zhoushan were collected and measured. Morphological results showed that these slender specimens were mainly brownish, usually mottled with pale. Standard length ranged from 117 mm to 213 mm with an average length of 180.3 mm. The above characters were consistent with S. schlegeli distributed in Japan but colored differently from and much smaller than typical S. acus reported in Europe. Thus, morphological studies revealed that this species was previously misidentified as S. acus and might be S. schlegeli in reality. In addition, a fragment of cytochrome oxidase subunit I （CO1） gene of mitochondrial DNA was also sequenced for species identification, and 15 COl sequences belonging to different Syngnathus species were also used for the molecular identification. CO1 sequences of our specimens had the minimum genetic distance from recognized S. schlegeli from Japan and clustered with it firstly. The phylogenetic analysis similarly suggested that the species previously identified as S. acus in the coastal waters of China was S. schlegeli actually.

Comparison of the In Vitro and In Vivo Toxic Effects of Three Sizes of Zinc Oxide(ZnO)Particles Using Flounder Gill(FG)Cells and Zebrafish Embryos

Nano-sized zinc oxide(n ZnO) particles are one kind of the most commonly used metal oxide nanoparticles(NPs). This study compared the cytotoxic and embryotoxic effects of three increasing sized ZnO particles(φ30 nm, 80-150 nm and 2 μm) in the flounder gill(FG) cells and zebrafish embryos, and analyzed the contribution of size, agglomeration and released Zn^(2+) to the toxic effects. All the tested ZnO particles were found to be highly toxic to both FG cells and zebrafish embryos. They induced growth inhibition, LDH release, morphological changes and apoptosis in FG cells in a concentration-, size-and time-dependent manner. Moreover, the release of LDH from the exposed FG cells into the medium occurred before the observable morphological changes happened. The ultrasonication treatment and addition of serum favored the dispersion of ZnO particles and alleviated the agglomeration, thus significantly increased the corresponding cytotoxicity. The released Zn^(2+) ions from ZnO particles into the extracellular medium only partially contributed to the cytotoxicity. All the three sizes of ZnO particles tested induced developmental malformations, decrease of hatching rates and lethality in zebrafish embryos, but size-and concentration-dependent toxic effects were not so obvious as in FG cells possibly due to the easy aggregation of ZnO particles in freshwater. In conclusion, both FG cells and zebrafish embryos are sensitive bioassay systems for safety assessment of ZnO particles and the environmental release of ZnO particles should be closely monitored as far as the safety of aquatic organisms is concerned.

Morphology and Molecular Phylogeny of Two Little-Known Species of Loxodes, L. kahli Dragesco & Njiné, 1971 and L. rostrum Müller, 1786(Protist, Ciliophora, Karyorelictea)

The morphology and phylogeny of two little-known species, Loxodes kahli Dragesco & Njiné, 1971 and L. rostrum Müller, 1786, isolated from freshwater muddy sediments in China, were investigated based on live features, infraciliature, and small subunit ribosomal DNA(SSU rD NA) sequence data. Loxodes kahli is distinguished from its congeners mainly by the number and arrangement of macronuclei(6-17 in one row) and the number of right somatic ciliary rows(11-26). The Chinese populations of L. kahli also exhibit differences with other populations in terms of the body size and the number of right ciliary rows. The characteristics of L. rostrum are consistent with those of previous studies except for the number of right ciliary rows(9-10). The studied species were redefined based on the new information and previous descriptions. This study also gave a brief morphological summary of the species in the genus Loxodes by an identification key. SSU rDNA sequence-based phylogenetic analyses revealed that both species are grouped with their congeners, supporting the monophyly of the genus Loxodes.

Transcriptome analysis of kelp Saccharina japonica unveils its weird transcripts and metabolite shift of main components at different sporophyte developmental stages

Saccharina japonica is an economically important cold water brown alga extensively cultivated in China. It is cultivated upside down under a floating rope net with its holdfast and meristematic area facing sunlight and UV irradiation and its blade tip toward dark, and other worse cultivation environmental factors also make S . japonic a face more stresses. In this study, S . japonica transcriptomes corresponding to its four developmental stages were analyzed. In total, 7 800 genes predicted in the genome were transcribed. We found that 1 208 of the 7 800 expressed and 2 697 annotated were virus associating genes. Of 778 diff erentially expressed genes (DEGs), 372 were annotatable and 209 were virus associating. Such portion of virus associating genes indicated that the S . japonica genome contained a large portion of active virus originating genes. It was found that the transcripts abundance associated with sugar biosynthesis was about 2.13 folds of all the expressed, indicating that the biosyntheses of structural and storage sugars were very important cellular processes. The total abundance of genes involved in the biosynthesis of alginate and laminarin were similar among all developmental stages, however, that of genes involved in the biosynthesis of mannitol increased about 2-folds from mushroom and adult stages to mature and aging stages. This trend explained our observation that the content of alginate was almost constant at diff erent development stages, while that of mannitol increased sharply. In addition, we found that a set of defense and cell recurring genes highly expressed and many of them expressed diff erentially among stages. On average, the sum abundance of the transcripts of these genes at four stages were 3.40-and 4.96-folds of all the annotated and all the expressed, respectively. This indicated that S . japonica sporophytes persistently respond possible pathogen and environment stresses. The findings are important for timing S . japonica harvest and amending the current cultivation mode.

Molecular phylogeny of oligotrich genera Omegastrombidium and Novistrombidium(Protozoa,Ciliophora) for the systematical relationships within Family Strombidiidae

The phylogeny of the oligotrich ciliates is currently a hot debate despite the availability of both morphological and molecular data.In the present paper,further small subunit rRNA(SS rRNA) genes were analyzed from the Genera Omegastrombidium and Novistrombidium,as well as from Strombidium,and combined with three new SS rRNA sequences from Strombidium basimorphum,S.sulcatum population QD-1,and Novistrombidium testaceum population GD.The phylogenetic positions of these organisms were inferred using Bayesian inference,Maximum Likelihood,and Maximum Parsimony methods.The main results are:(1) the SS rRNA gene sequence analyses match the recent findings about the molecular evolution of oligotrichs,indicating that the family Strombidiidae is paraphyletic;(2) the Genus Omegastrombidium is separated from the Genus Strombidium,as shown in recent cladistic analyses;(3) morphospecies in Genus Novistrombidium,based on similarity of somatic ciliature,are separated from each other in all topological trees,indicating that this genus could be a paraphyletic group;(4) the molecular data indicate a possibility of paraphyly for the genus Strombidium;and(5) the similarities of the SS rRNA gene of specimens identified as S.sulcatum and S.inclinatum are 99.8%-100%.However,present knowledge on the oligotrichs sensu stricto is still insufficient and further studies based on both molecular and other technologies are required.

Planktonic protist communities in semi-enclosed mariculture waters: temporal dynamics of functional groups and their responses to environmental conditions

The functional groups of planktonic protist communities and their responses to the changes of environmental conditions were investigated in a semi-enclosed shrimp-farming pond in Qingdao,Shandong Province,China,during a six-month study period （a complete shrimp-culture cycle） from May to October 2002.The results reveal that： （1） the protist communities represented five trophic and functional groups of the species identified,about 60% were photoautotrophs,20% algivores,12% bacterivores,5% raptors and about 3% non-selectives;（2） the photoautotrophs,algivores and bacterivores were the primary contributors to the changes in the protist communities in short temporal scales,the succession of dominance typically being bacterivores→photoautotrophs→algivores,with the raptors dominating the protist communities in a single sample （early June）;（3） the photoautotrophs and non-selectives were the primary contributors to the peak of protist abundance in early October whereas the photoautotrophs,bacterivores,raptors and non-selectives mainly gave rise to two bimodal peaks of biomass in July and October respectively;（4） five functional groups of protist communities represented significant correlations with water nutrients （i.e.,NH 3-N,NO 3-N,and PO 4 ）,either alone or in combination with temperature,of which algivores and raptors were strongly correlated with phosphate and the concentration of Chl a,while bacterivores were strongly related to nitrogen and the concentration of bacteria.These findings confirm that planktonic protists are potentially useful bioindicators of water quality in the semi-enclosed mariculture system.

Triterpenoid saponin biosynthesis genes and their expression patterns during the development of sea cucumber Apostichopus japonicus

Sea cucumbers are echinoderm species with a leathery skin and an elongated body.Natural compounds,including saponins,have been previously isolated from sea cucumber.The majority of saponins derived from this organism typically belong to the triterpene glycosides,which exhibit various biological effects(e.g.,antifungal,cytotoxic,hemolytic,and cytostatic immunomodulatory activities).In the present study,30 saponin biosynthesis enzymes,namely 2 AACTs,2 FPSs,2 HMGSs,2 OSCs,1 SS,2 SEs,and 19 UGTs,were found in the genome of sea cucumber Apostichopus japonicus.Compared with upstream saponin biosynthesis enzymes(i.e.,AACTs,FPSs,HMGSs,OSCs,and SSs),the downstream saponin biosynthesis enzymes(SEs and UGTs)shared lower amino acid sequence similarity with the corresponding genes in other echinoderms.It was proposed that the enzyme structures comprised bothα-helices andβ-sheets.Notably,only a low percentage ofβ-sheets were present in FPSs,OSCs,and SS.The saponin biosynthesis enzymes showed dynamic expression patterns during five critical developmental stages of A.japonicus(fertilized oocytes,blastula,gastrula,doliolaria,and penractula).The present study involved elucidation of putative saponin biosynthesis pathways in sea cucumber and provides a valuable platform for further investigation of saponin biosynthesis in echinoderms.

Temporal species distributions of planktonic protist communities in semi-enclosed mariculture waters and responses to environmental stress

In order to evaluate the relationships between temporal species succession of planktonic protists and physical-chemical parameters in semi-enclosed mariculture waters, species distributions in response to environmental stress were investigated in a shrimp-farming pond near Qingdao, China during a complete shrimp-culture cycle （May to October 2002）. A clear temporal succession in species distribution was found over the complete farming cycle. For example, before the introduction of the shrimp larvae there was low-variability of species distribution in the protist communities whereas during the stages immediately after, there was higher variability in species composition. Multiple linear/logistic regression analyses demonstrate that 12 protist taxa （e.g., Gyrodinium spirale, Teleaulax acuta, Prorocentrum spp. and Mesodinium pupula） were related to the nutrients, in particular ammonia and phosphates, alone or in combination with water temperature. These results suggest that temporal variations in species distribution of planktonic protist communities might be used in assessing water quality of semi-enclosed mariculture waters.

Hatschek's pit and origin of pituitary gland

Pituitary gland,or pituitary for short,is characteristic of all vertebrates.As a“master gland”controlling a multitude of important functions in the body,its evolutionary origin has been an object of investigations of evolutionary biology for two centuries.Previous morphological,ultrastructural and immunohistochemical studies suggested the homology of the Hatschek’s pit of amphioxus and vertebrate pituitary.Developmental genetics study showed that the development of Hatschek’s pit and vertebrate pituitary is both subject to regulation by the common genes such as Pit1,Lhx3 and BMP3b.Our recent studies demonstrated that the Hatschek’s pit is able to secrete growth hormone(GH)-like hormone and thyroid-stimulating hormone(TSH)-like hormone that both play functions similar to vertebrate GH and TSH.We thus think that the emergence of Hatschek’s pit represents one of important events during endocrine network evolution,which laid a foundation for the subsequent formation of a hypothalamic-pituitary system in vertebrates.

Assessing mariculture water quality with the structural and functional characteristics of a ciliate community

Ciliated protozoa play important roles in micro-ecosystems, especially in marine biotopes. However, few studies have been carried out on the periphytic, or aufwuch, forms in mariculture waters so far. In this study, we sampled periphytic ciliate communities in two closed mariculture ponds (ponds CP1 and CP2) and a natural seawater reservoir (pond RP) using a glass slide method to evaluate their colonizing processes and general ecological features, as well as their application as water quality indicators. We analyzed species compositions, structural parameters (species number, richness, diversity, evenness, abundance and dBP) and functional parameters (G, Seq and T90%). Pond RP was characterized by higher levels of structural parameters (except for abundance and dBP) and more equal proportion of the major taxonomic groups. The values of Seq were significantly higher in pond RP and similar in both pond CP1 and CP2. It was also demonstrated that environmental factors, including NO2-H, NO3-H, NH3-H, soluble reactive phosphate, temperature and pH, were the first principal factors affecting the communities. Among them, temperature and chemical factors were all significantly and negatively correlated with species number (P<0.01), richness (P<0.01), diversity (P<0.01), and positive correlated with abundance (P<0.01). Opposite correlations between pH and structural parameters were observed. This study showed that there were significant differences in species composition, structural parameters and functional parameters of the periphytic ciliate communities among the ponds, which were in agreement with the water quality. Results of this study confirmed the periphytic ciliate communities to be useful bioindicators of water quality in intensive mariculture waters.