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Morphology and Phylogeny of the Soil Ciliate Metopus Yantaiensis N. Sp

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Morphology and Phylogeny of the Soil Ciliate Metopus Yantaiensis N. Sp Journal of Eukaryotic Microbiology ISSN 1066-5234 ORIGINAL ARTICLE Morphology and Phylogeny of the Soil Ciliate Metopus yantaiensis n. sp. (Ciliophora, Metopida), with Identification of the Intracellular Bacteria Atef Omara,b, Qianqian Zhanga, Songbao Zoua,c & Jun Gonga,c a Laboratory of Microbial Ecology and Matter Cycles, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China b Department of Zoology, Al-Azhar University, Assiut 71524, Egypt c University of Chinese Academy of Sciences, Beijing 100049, China Keywords ABSTRACT Anaerobic ciliates; Armophorea; digestion- resistant bacteria; Metopus contortus; The morphology and infraciliature of a new ciliate, Metopus yantaiensis n. sp., Metopus hasei. discovered in coastal soil of northern China, were investigated. It is distin- guished from its congeners by a combination of the following features: nuclear Correspondence apparatus situated in the preoral dome; 18–21 somatic ciliary rows, of which J. Gong, Yantai Institute of Coastal Zone three extend onto the preoral dome (dome kineties); three to five distinctly Research, Chinese Academy of Sciences, elongated caudal cilia, and 21–29 adoral polykinetids. The 18S rRNA genes of Yantai 264003, China this new species and two congeners, Metopus contortus and Metopus hasei, Telephone number: +86-535-2109123; were sequenced and phylogenetically analyzed. The new species is more clo- FAX number: +86-535-2109000; sely related to M. hasei and the clevelandellids than to other congeners; both e-mail: [email protected] the genus Metopus and the order Metopida are not monophyletic. In addition, the digestion-resistant bacteria in the cytoplasm of M. yantaiensis were identi- Received: 13 January 2017; revised 2 March fied, using a 16S rRNA gene clone library, sequencing, and fluorescence 2017; accepted March 8, 2017. in situ hybridization. The detected intracellular bacteria are affiliated with Sphin- Early View publication April 10, 2017 gomonadales, Rhizobiales, Rickettsiales (Alphaproteobacteria), Pseudomonas (Gammaproteobacteria), Rhodocyclales (Betaproteobacteria), Clostridiales (Fir- doi:10.1111/jeu.12411 micutes), and Flavobacteriales (Bacteroidetes). MEMBERS of the ciliate genus Metopus Claparede and hydrogenosomes) instead of classical mitochondria as an Lachmann, 1858 are widely distributed in anaerobic and adaptation to the anaerobic environment (Hackstein et al. microaerobic freshwater, terrestrial, and marine habitats 1999; Muller€ 1988). The anaerobic habitat and the special (Bourland and Wendell 2014; Bourland et al. 2014, 2016; organelles have motivated many scientists to study the Corliss 1979; Da Silva-Neto et al. 2016; Jankowski 1964a, endosymbionts of Metopus, of which most focused on b; Lynn 2008). Despite about 81 species and 25 sub- the methanogenic archaea (van Bruggen et al. 1984, 1986; species of this genus having been recorded (Roskov et al. Embley and Finlay 1993; Embley et al. 1992a,b; Fenchel 2016), only a few Metopus species have been investi- and Finlay 1991; Muller€ 1993; Narayanan et al. 2009). gated, using modern morphological methods and sequenc- However, still little is known about the bacteria associated ing for phylogenetic inference. Morphologically, this genus with these organisms. can be easily recognized because of the anteriorly twisted In this study, we isolated and investigated the mor- body and the oblique or spiraling adoral zone of polykine- phology and ciliary pattern of a new soil metopid spe- tids, which is overhung by the preoral dome (Foissner cies from China. We sequenced the 18S rRNA gene of et al. 1992; Jankowski 1964a,b; Kahl 1927; Vd’acn y and this new species and two known Metopus species. Fur- Foissner 2017). thermore, the intracellular bacteria of the new ciliate Cell biology and ecology of Metopus species are also species, also called digestion-resistant bacteria (DRB; characteristic among ciliates. They have symbiotic prokary- Gong et al. 2016), were identified, using molecular otes and hydrogen-forming organelles (called methodologies. © 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists 792 Journal of Eukaryotic Microbiology 2017, 64, 792–805 Omar et al. Metopus yantaiensis and Associated Bacteria cycles of denaturation at 94 °C for 1 min, annealing at MATERIALS AND METHODS 52 °C for 1 min, extension at 72 °C for 2 min; and then a final extension step at 72 °C for 10 min. To inspect the Collection and ciliate cultivation ingested but not digested bacteria and archaea within Metopus yantaiensis n. sp. was discovered in a coastal soil these ciliates, we amplified the bacterial 16S rDNA, using sample originally from an apple orchard near Yantai City, the primers 27F (5ʹ-AGAGTTTGATCMTGGCTCAG-3ʹ) and Shandong, China (37°57ʹ73″N, 120°66ʹ51″E). The upper 1492R (5ʹ- ACGGCTACCTTGTTACGACTT-3ʹ), and the fol- layer of the soil with a small amount of litter was collected, lowing program: prerun of 5 min at 94 °C; 30 cycles of air-dried for two weeks, and stored in a plastic bag. Later, denaturation at 94 °C for 90 s, annealing at 55 °C for the sample was investigated, using the nonflooded Petri 1 min, extension at 72 °C for 1 min; and then a final dish method as described by Foissner et al. (2002), with extension step at 72 °C for 10 min. The archaeal 16S some dried and sterilized pieces of grass being added and rDNA was amplified with the Archaea-specific primer 21F mixed to increase the organic matter and filter capacity of (50-TCCGGTTGATCCYGCCGG-30) and the universal primer the very fine-grained soil. From the nonflooded Petri dish 1492R. The amplified PCR products were purified, using culture (NFPC), a few ciliate cells were picked up with a the TIANgel Midi Purification Kit (Tiangen, Shanghai, micropipette, washed and incubated into mineral water China), and cloned into a PTZ57R/T vector, using InsTA- supplied with sterilized chopped grass to establish the raw clone PCR Cloning Kit (Thermo Scientific, Shanghai, cultures (RC). Some cells were picked from the RC, using China), and then transferred into Escherichia coli DH5a a fine pipette, and transferred onto a microscope slide with cells. Multiple positive clones with ciliate 18S (20) and a few drops of filtered water; resting cysts were then bacterial 16S rRNA (46) gene inserts were selected ran- formed after maintaining for a few days in a wet chamber. domly and screened, using restricted fragment length Two known species, Metopus contortus (Quennerstedt, polymorphism (RFLP) analysis with the restriction enzyme 1867) Kahl, 1932 and Metopus hasei Sondheim, 1929 HaeIII under the conditions recommended by the supplier were sampled from marine anaerobic sediments of the (Fast digest, Thermo Scientific). Sequencing in both direc- Swan Lake lagoon, Rongcheng, and moss from the Kunyu tions was carried out on an ABI 377 automated sequencer Mountain, Yantai, Shandong, China, respectively. (Sangon, Shanghai, China). Morphological observations Phylogenetic analysis Living cells were studied, using bright field and differential The new 18S rRNA gene sequences of M. yantaiensis n. interference contrast microscopy at magnifications of sp., M. contortus, and M. hasei, along with metopid, 100–1,000X. The ciliary and nuclear patterns were clevelandellid, caenomorphid, litostomatean and spirotrich revealed, using the protargol impregnation method of Wil- sequences retrieved from the GenBank database, were bert (1975). Counts and measurements of prepared speci- aligned, using MAFFT v.7 (Katoh and Standley 2013). mens were performed at a magnification of 1,000X. Three karyorelicteans were used as the outgroup species. Drawings of live cells were based on free-hand sketches, The alignment was refined manually to excise hypervari- while those of impregnated specimens were made, using able regions, using BioEdit 7.0 (Hall 1999), resulting in 21 a drawing device. taxa and 1,643 nucleotide positions. For the newly obtained bacterial 16S rRNA gene sequences, we removed chimeric sequences identified by Bellerophon DNA extraction, PCR amplification, clone libraries, and (Huber et al. 2004). Closely related bacterial sequences sequencing were retrieved from the GenBank and aligned with these To extract genomic DNA of the protists and associated newly obtained. The final alignment for the bacteria com- bacteria, ciliate cells from the raw cultures were washed prised 43 taxa and 1,423 nucleotide positions. three times with 0.22 lm-filtered mineral water, and then The maximum likelihood (ML) trees of the 18S and 16S starved for about 18 h to allow digesting bacterial preys. rRNA genes were constructed, using RAxML-HPC v7.2.5 The cells were washed again to minimize contamination. (Stamatakis et al. 2008). Nodal supports in ML analyses The individuals were transferred into 0.2 ml PCR tubes came from 1,000 bootstrap replicates, using heuristic with a small drop of water (0.5 ll) for DNA extraction, and searches. Both analyses employed the GTR + G + I up to 20 cells were mounted on slides for subsequent nucleotide substitution model, selected according to the FISH assays. Akaike information criterion in jModelTest 2.1 (Darriba Genomic DNA was extracted with REDExtract-N-Amp et al. 2012). The Bayesian inference (BI) analysis was per- Tissue PCR Kit (Sigma, St. Louis, MO) according to Gong formed, using MrBayes v.3.2.1 (Ronquist and Huelsen- et al. (2014). The 18S rRNA gene was PCR amplified with beck 2003) for both the 16S and 18S rRNA genes. Markov the primers 82F (5ʹ-GAAACTGCGAATGGCTC-3ʹ) and Euk B chain Monte Carlo (MCMC) simulations were run, with (5ʹ-TGATCCTTCTGCAGGTTCACCTAC-3ʹ) or 1520R (50- two sets of four chains, using the default settings, for CYGCAGGTTCACCTAC-3ʹ). The PCR reactions were per- 3,000,000 generations, sampling every 1,000 generations. formed in a thermal cycler (Biometra, Gottingen,€ Germany) The first 25% of sampled trees were considered burn-in with the following program: prerun of 5 min at 94 °C; 35 and discarded, and the remaining trees were used to © 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists Journal of Eukaryotic Microbiology 2017, 64, 792–805 793 Metopus yantaiensis and Associated Bacteria Omar et al.
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