Diversity of oligotrich ciliates (Ciliophora, Spirotrichea) in the northern coast of South China Sea as revealed in LSU rDNA sequences -- Journal of Oceanology and Limnology,2020,38(1):156-167

	Cite this paper:
	LU Kaihui, LIU Weiwei, Alan WARREN, XU Yusen, ZHU Changyu, ZHAO Yan, YI Zhenzhen. Diversity of oligotrich ciliates (Ciliophora, Spirotrichea) in the northern coast of South China Sea as revealed in LSU rDNA sequences[J]. Journal of Oceanology and Limnology, 2020, 38(1): 156-167

Diversity of oligotrich ciliates (Ciliophora, Spirotrichea) in the northern coast of South China Sea as revealed in LSU rDNA sequences

LU Kaihui¹, LIU Weiwei², Alan WARREN³, XU Yusen¹, ZHU Changyu¹, ZHAO Yan⁴, YI Zhenzhen¹

1 Laboratory of Protozoology, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China;
2 Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China;
3 Department of Life Sciences, Natural History Museum, London SW7 5BD, United K ingdom;
4 College of Life Sciences, Capital Normal University, Beijing 100048, China

Abstract:

Although the taxonomy of oligotrich ciliates has been widely investigated, yet the species diversity remains poorly known. We newly designed a pair of oligotrich-specific LSU rDNA primers covering the 600-bp D1/D2 region, and it was effective for detecting oligotrich species. Using the primers, we constructed the cloning libraries to investigate the species diversity of oligotrichs in the northern coastal waters of the South China Sea. In total, 165 oligotrich sequences were obtained from five widely separated sampling sites. Sixty operational taxonomic units (OTUs) were obtained at 99% similarity threshold, and low-abundance OTUs with no more than two sequences contributed most of these (about 78%). Our findings are consistent with previous morphological studies, Strombidium was found the most abundant and widely distributed genus in this area. In addition, the BLAST search in the NCBI database resulted in 95% OTUs matching with named oligotrich species in similarity below 99%. Therefore, oligotrich morphospecies diversity has been underestimated as low-abundance species, and the LSU rDNA oligotrich sequence database needs to be better promoted.

Key words: diversity|low-abundance species|oligotrich ciliates|operational taxonomic units (OTUs)

Received: 2019-01-24 Revised:

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References:
Agatha S, Strüder-Kypke M C, Beran A, Lynn D H. 2005.Pelagostrobilidium neptuni (Montagnes and Taylor, 1994)and Strombidium biarmatum nov. spec. (Ciliophora, Oligotrichea):phylogenetic position inferred from morphology, ontogenesis, and gene sequence data.European Journal of Protistology, 41(1):65-83.
Agatha S. 2004. A cladistic approach for the classification of oligotrichid ciliates (Ciliophora:Spirotricha). Acta Protozoologica, 43(3):201-217.
Agatha S. 2011. Global diversity of aloricate Oligotrichea(Protista, Ciliophora, Spirotricha) in marine and brackish sea water. PLoS One, 6(8):e22466.
Azam F, Fenchel T, Field J G, Gray J S, Meyer-Reil L A, Thingstad F. 1983. The ecological role of water-column microbes in the sea. Marine Ecology Progress Series, 10(3):257-263.
Bachy C, Dolan J R, López-García P, Deschamps P, Moreira D. 2013. Accuracy of protist diversity assessments:morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study.The ISME Journal, 7(2):244-255.
Bachy C, Gómez F, López-García P, Dolan J R, Moreira D. 2012. Molecular phylogeny of tintinnid ciliates(Tintinnida, Ciliophora). Protist, 163(6):873-887.
Bachy C, Moreira D, Dolan J R, López-García P. 2014.Seasonal dynamics of free-living tintinnid ciliate communities revealed by environmental sequences from the North-West Mediterranean Sea. FEMS Microbiology Ecology, 87(2):330-342.
Caporaso J G, Kuczynski J, Stombaugh J, Bittinger K, Bushman F D, Costello E K, Fierer N, Peña A G, Goodrich J K, Gordon J I, Huttley G A, Kelley S T, Knights D, Koenig J E, Ley R E, Lozupone C A, McDonald D, Muegge B D, Pirrung M, Reeder J, Sevinsky J R,Turnbaugh P J, Walters W A, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5):335-336.
Chen W P. 2014. The species composition and Taxonomic study of ciliated protozoa in mangrove wetlands of the Futian National Nature Reserve, Shenzhen. South China Normal University, Guangzhou, China. (in Chinese with English abstract)
Countway P D, Gast R J, Savai P, Caron D A. 2005. Protistan diversity estimates based on 18S rDNA from seawater incubations in the western North Atlantic. The Journal of Eukaryotic Microbiology, 52(2):95-106.
Demir N, Sayood K. 1998. Joint source/channel coding for variable length codes. In:Proceedings DCC'98 Data Compression Conference. IEEE, Snowbird, UT, USA.p.139-148.
Díez B, Pedrós-Alió C, Massana R. 2001. Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Applied and Environmental Microbiology, 67(7):2 932-2 941.
Dinauer D, Bollmer J, Chen Z T, Bialozynski C, Shi J, Conradson S. 2014. P086:improved ion torrent sequencing chemistry enables rapid turn around and 600BP reads. Human Immunology, 75 Suppl. 1:112.
Doherty M, Costas B A, McManus G B, Katz L A. 2007.Culture-independent assessment of planktonic ciliate diversity in coastal northwest Atlantic waters. Aquatic Microbial Ecology, 48(2):141-154.
Doherty M, Tamura M, Vriezen J A C, McManus G B, Katz L A. 2010. Diversity of Oligotrichia and Choreotrichia ciliates in coastal marine sediments and in overlying plankton. Applied and Environmental Microbiology, 76(12):3 924-3 935.
Dong J, Shi F, Li H, Zhang X M, Hu X Z, Gong J. 2014. SSU rDNA sequence diversity and seasonally differentiated distribution of nanoplanktonic ciliates in neritic Bohai and Yellow Seas as revealed by T-RFLP. PLoS One, 9(7):e102640.
Dunthorn M, Stoeck T, Clamp J, Warren A, Mahé F. 2014.Ciliates and the rare biosphere:a review. The Journal of Eukaryotic Microbiology, 61(4):404-409.
Edgcomb V P, Kysela D T, Teske A, de Vera Gomez A, Sogin M L. 2002. Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proceedings of the National Academy of Sciences of the United States of America, 99(11):7 658-7 662.
Endo Y, Hasumoto H, Taniguchi A. 1983. Microzooplankton standing crop in the western subtropical pacific off the Bonin Islands in winter, 1980. Journal of the Oceanographical Society of Japan, 39(4):185-191.
Foissner W. 2014. An update of ‘Basic light and scanning electron microscopic methods for taxonomic studies of ciliated protozoa’. International Journal of Systematic and Evolutionary Microbiology, 64(1):271-292.
Gao F, Li J M, Song W, Xu D P, Warren A, Yi Z Z, Gao S. 2016a. Multi-gene-based phylogenetic analysis of oligotrich ciliates with emphasis on two dominant groups:cyrtostrombidiids and strombidiids (Protozoa, Ciliophora). Molecular Phylogenetics and Evolution, 105:241-250.
Gao F, Warren A, Zhang Q Q, Gong J, Miao M, Sun P, Xu D P, Huang J, Yi Z Z, Song W B. 2016b. The all-data-based evolutionary hypothesis of ciliated protists with a revised classification of the phylum Ciliophora (Eukaryota, Alveolata). Scientific Reports, 6:24874.
Gao S, Gong J, Lynn D, Lin X F, Song W B. 2009. An updated phylogeny of oligotrich and choreotrich ciliates (Protozoa, Ciliophora, Spirotrichea) with representative taxa collected from Chinese coastal waters. Systematics and Biodiversity, 7(2):235-242.
Grattepanche J D, Santoferrara L F, Andrade J, Oliverio A M, McManus G B, Katz L A. 2013. Distribution and diversity of oligotrich and choreotrich ciliates assessed by morphology and DGGE in temperate coastal waters.Aquatic Microbial Ecology, 71(3):211-221.
Hall T A. 1999. BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41:95-98.
Huang J B, Zhang T T, Zhang Q Q, Li Y, Warren A, Pan H B, Yan Y. 2018. Further insights into the highly derived haptorids (Ciliophora, Litostomatea):phylogeny based on multigene data. Zoologica Scripta, 47(2):231-242.
Jung J H, Kim S, Ryu S, Kim M S, Baek Y S, Kim S J, Choi J K, Park J K, Min G S. 2012. Development of singlenucleotide polymorphism-based phylum-specific PCR amplification technique:application to the community analysis using ciliates as a reference organism. Molecules and Cells, 34(4):383-391.
Knowlton N. 1993. Sibling species in the sea. Annual Review of Ecology and Systematics, 24:189-216.
Kumar S, Stecher G, Tamura K. 2016. MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7):1 870-1 874.
Leakey R J G, Burkill P H, Sleigh M A. 1996. Planktonic ciliates in the northwestern Indian Ocean:their abundance and biomass in waters of contrasting productivity. Journal of Plankton Research, 18(6):1 063-1 071.
Lee E S, Shin M K, Kim Y O. 2011. Morphological descriptions of four oligotrich ciliates (Ciliophora:Oligotrichia) from southern coast of Korea. Korean Journal of Systematic Zoology, 27(2):131-141.
Li J M, Liu W W, Gao S, Warren A, Song W B. 2013.Multigene-based analyses of the phylogenetic evolution of oligotrich ciliates, with consideration of the Internal Transcribed Spacer 2 secondary structure of three systematically ambiguous genera. Eukaryotic Cell, 12(3):430-437.
Liu W W, Xu D P, Lin X F, Li J Q, Gong J, Al-Rasheid K A S, Song W B. 2010. Novistrombidium sinicum n. sp. and Novistrombidium orientale n. sp. (Protozoa:Ciliophora):two new oligotrich ciliates from a mangrove wetland,South China. The Journal of Eukaryotic Microbiology, 56(5):459-465.
Liu W W, Xu D P, Ma H G, Al-Farraj S A, Warren A, Yi Z Z. 2016. Taxonomy and molecular systematics of three oligotrich (s.l.) ciliates including descriptions of two new species, Strombidium guangdongense sp. nov. and Strombidinopsis sinicum sp. nov. (Protozoa, Ciliophora).Systematics and Biodiversity, 14(5):452-465.
Liu W W, Yi Z Z, Li J Q, Warren A, Al-Farraj S A, Lin X F. 2013. Taxonomy, morphology and phylogeny of three new oligotrich ciliates (Protozoa, Ciliophora, Oligotrichia)from southern China. International Journal of Systematic and Evolutionary Microbiology, 63(12):4 805-4 817.
Liu W W, Yi Z Z, Lin X F, Warren A, Song W B. 2012.Phylogeny of three choreotrich genera (Protozoa, Ciliophora, Spirotrichea), with morphological, morphogenetic and molecular investigations on three strobilidiid species. Zoologica Scripta, 41(4):417-434.
Liu W W, Yi Z Z, Warren A, Al-Rasheid K A S, Al-Farraj S A, Lin X F, Song W B. 2011. Taxonomy, morphology and molecular systematics of a new oligotrich ciliate, Williophrya maedai gen. nov., sp. nov., with redescriptions of Strombidium basimorphum and Pseudotontonia simplicidens (Protozoa, Ciliophora, Oligotrichia).Systematics and Biodiversity, 9(3):247-258.
Liu W W, Yi Z Z, Xu D P, Clamp J C, Li J Q, Lin X F, Song W B. 2015. Two new genera of planktonic ciliates and insights into the evolution of the family Strombidiidae(Protista, Ciliophora, Oligotrichia). PLoS One, 10(6):e0131726.
Liu W W. 2011. Studies on the taxonomy and phylogeny of oligotrich ciliates from the coastal waters off Guangdong.South China Normal University, Guangzhou, China. (in Chinese with English abstract)
Martin A J, Montagnes D J S. 1993. Winter ciliates in a British Columbian fjord:six new species and an analysis of ciliate putative prey. The Journal of Eukaryotic Microbiology, 40(5):535-549.
McManus G B, Katz L A. 2009. Molecular and morphological methods for identifying plankton:what makes a successful marriage? Journal of Plankton Research, 31(10):1 119-1 129.
McManus G B, Xu D P, Costas B A, Katz L A. 2010. Genetic identities of cryptic species in the Strombidium stylifer/apolatum/oculatum cluster, including a description of Strombidium rassoulzadegani n. sp. The Journal of Eukaryotic Microbiology, 57(4):369-378.
Modeo L, Petroni G, Rosati G, Montagnes D J S. 2003. A multidisciplinary approach to describe protists:redescriptions of Novistrombidium testaceum Anigstein 1914 and Strombidium inclinatum Montagnes, Taylor, and Lynn 1990 (Ciliophora, Oligotrichia). The Journal of Eukaryotic Microbiology, 50(3):175-189.
Nylander J A A. 2004. MrModeltest Version 2. Program Distributed by the Author. Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
Pierce R W, Turner J T. 1992. Ecology of planktonic ciliates in marine food webs. Review Aquatic Sciences, 6(2):139-181.
Pitta P, Giannakourou A, Christaki U. 2001. Planktonic ciliates in the oligotrophic Mediterranean Sea:longitudinal trends of standing stocks, distributions and analysis of food vacuole contents. Aquatic Microbial Ecology, 24(3):297-311.
Ren L, Zhu B Q, Zhang Y B, Wang H Y, Li C Y, Su Y H, Ba C F. 2004. The research of applying primer premier 5.0 to design PCR primer. Journal of Jinzhou Medical College, 25(6):43-46. (in Chinese with English abstract)
Santoferrara L F, Alder V V, McManus G B. 2017. Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea). Molecular Phylogenetics and Evolution, 112:12-22.
Santoferrara L F, Grattepanche J D, Katz L A, McManus G B. 2016. Patterns and processes in microbial biogeography:do molecules and morphologies give the same answers?The ISME Journal, 10(7):1 779-1 790.
Santoferrara L F, McManus G B, Alder V A. 2013. Utility of genetic markers and morphology for species discrimination within the Order Tintinnida (Ciliophora, Spirotrichea).Protist, 164(1):24-36.
Santoferrara L F, Tian M, Alder V A, McManus G B. 2015.Discrimination of closely related species in tintinnid ciliates:new insights on crypticity and polymorphism in the genus Helicostomella. Protist, 166(1):78-92.
Shen Z. 2012. Studies on the taxonomy and phylogeny of Peritrichia ciliates from coastal waters off Guangdong.South China Normal University, Guangzhou, China. (in Chinese with English abstract)
Sheng Y L, He M, Zhao F Q, Shao C, Miao M. 2018.Phylogenetic relationship analyses of complicated class Spirotrichea based on transcriptomes from three diverse microbial eukaryotes:Uroleptopsis citrina, Euplotes vannus and Protocruzia tuzeti. Molecular Phylogenetics and Evolution, 129:338-345.
Song W, Li J M, Liu W W, Al-Rasheid K A S, Hu X Z, Lin X F. 2015a. Taxonomy and molecular phylogeny of four Strombidium species, including description of S.pseudostylifer sp. nov. (Ciliophora, Oligotrichia).Systematics and Biodiversity, 13(1):76-92.
Song W, Li J M, Liu W W, Jiang J M, Al-Rasheid K A S, Hu X Z. 2013. Taxonomy, morphology and molecular systematics of three oligotrich ciliates, including a description of Apostrombidium parakielum spec. nov.(Ciliophora, Oligotrichia). International Journal of Systematic and Evolutionary Microbiology, 63(3):1 179-1 191.
Song W, Wang L, Li L F, Al-Farraj S A, Aleidan A, Smith S, Hu X Z. 2018. Morphological characterizations of four species of Parallelostrombidium (Ciliophora, Oligotrichia), with a note on the phylogeny of the genus.The Journal of Eukaryotic Microbiology, 65(5):679-693.
Song W, Warren A, Hu X Z. 2009. Free-Living Ciliates in the Bohai and Yellow Seas, China. Science Press, Beijing. 518p.
Song W, Zhao X L, Liu W W, Hu X Z, Al-Farraj S A, AlRasheid K A S, Song W B, Warren A. 2015b. Biodiversity of oligotrich ciliates in the South China Sea:description of three new Strombidium species (Protozoa, Ciliophora, Oligotrichia) with phylogenetic analyses. Systematics and Biodiversity, 13(6):608-623.
Stoeck T, Bass D, Nebel M, Christen R, Jones M D M, Breiner H W, Richards T A. 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology, 19(S1):21-31.
Stoeck T, Przybos E, Dunthorn M. 2014. The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates.Molecular Ecology Resources, 14(3):458-468.
Strüder-Kypke M C, Lynn D H. 2010. Comparative analysis of the mitochondrial cytochrome c oxidase subunit I (COI)gene in ciliates (Alveolata, Ciliophora) and evaluation of its suitability as a biodiversity marker. Systematics and Biodiversity, 8(1):131-148.
Su L, Zhang Q Q, Gong J. 2018. Development and evaluation of specific PCR primers targeting the ribosomal DNAinternal transcribed spacer (ITS) region of peritrich ciliates in environmental samples. Journal of Oceanology and Limnology, 36(3):818-826.
Tautz D, Arctander P, Minelli A, Thomas R H, Vogler A P. 2003. A plea for DNA taxonomy. Trends in Ecology & Evolution, 18(2):70-74.
Tucker S J, McManus G B, Katz L A, Grattepanche J D. 2017.Distribution of abundant and active planktonic ciliates in coastal and slope waters off New England. Frontiers in Microbiology, 8:2178.
Wang R, Song W, Yi Z Z, Al-Rasheid K A S, Lin X Z. 2018.Morphology and molecular phylogeny of two new species of Spirostrombidium (Ciliophora, Oligotrichia), with a key to the species of Spirostrombidium. Systematics and Biodiversity, 16(8):743-756.
Wang Y R, Wang C D, Jiang Y H, Katz L A, Gao F, Yan Y. 2019. Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny. Science China Life Sciences, 62(2):203-214.
Worden A Z, Follows M J, Giovannoni S J, Wilken S, Zimmerman A E, Keeling P J. 2015. Rethinking the marine carbon cycle:factoring in the multifarious lifestyles of microbes. Science, 347(6223):1257594.
Wu L, Jiao X X, Shen Z, Yi Z Z, Li J Q, Warren A, Lin X F. 2017. New taxa refresh the phylogeny and classification of pleurostomatid ciliates (Ciliophora, Litostomatea).Zoologica Scripta, 46(2):245-253.
Xu D P. 2007. Taxonomy studies on marine oligotrich ciliates(Protozoa:Ciliophora) from coastal waters off Qingdao, China. Ocean University of China, Qingdao, China. (in Chinese with English abstract)
Yi Z Z, Dunthorn M, Song W B, Stoeck T. 2010. Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea).Molecular Phylogenetics and Evolution, 57(2):937-941.
Zhang Q Q, Yi Z Z, Xu D P, Al-Rasheid K A S, Gong J, Song W B. 2010. Molecular phylogeny of oligotrich genera Omegastrombidium and Novistrombidium (Protozoa, Ciliophora) for the systematical relationships within family Strombidiidae. Chinese Journal of Oceanology and Limnology, 28(4):769-777.
Zhang Q Q. 2012. On the molecular phylogeny of seven subclasses in the phylum Ciliophora. Ocean University of China, Qingdao:China. (in Chinese with English abstract)
Zhao F, Xu K D. 2016. Biodiversity patterns of soil ciliates along salinity gradients. European Journal of Protistology, 53:1-10.
Zhao Y, Yi Z Z, Gentekaki E, Zhan A B, Al-Farraj S A, Song W B. 2016. Utility of combining morphological characters, nuclear and mitochondrial genes:an attempt to resolve the conflicts of species identification for ciliated protists.Molecular Phylogenetics and Evolution, 94:718-729.
Zhao Y, Yi Z Z, Warren A, Song W B. 2018. Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes(Alveolata, Ciliophora). Proceedings of the Royal Society B:Biological Sciences, 285(1871):20172159.