Microplankton communities of three coastal sites of Qingdao,Shandong Province,China were investigated using RAPD(random amplified polymorphic DNA) molecular markers and morphological observations.Eight RAPD-primers ...Microplankton communities of three coastal sites of Qingdao,Shandong Province,China were investigated using RAPD(random amplified polymorphic DNA) molecular markers and morphological observations.Eight RAPD-primers were selected to amplify the DNA polymorphy.The genetic distances inferred from the pairwise similarities were calculated for the phylogenetic tree construction.Meantime,the traditional microscopic determination,a way of visualizing the species composition,was performed to detect the major taxa of microplanktons from all samples.Results showed that:(1) the band sharing index values were in the range of 0.504 2-0.763 2 among samples from the same sampling site at different time scales,while 0.406 5-0.685 7 among the samples from different stations at the same time scales,indicating that spatial variations of microplankton communities were more pronounced than temporal ones;(2) samples from the same station basically clustered together,corresponding to the geographic distribution of the sampling sites;(3) diversity derived from genetic and morphological data did not correspond with each other well.展开更多
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 regio...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.展开更多
One new marine oligotrich ciliate, Omegastrombidium hongkongense n. sp., was isolated from a bloom of Noctiluca scuntillans near Port Shelter, Hong Kong. The morphology and infraciliature of this new species were stud...One new marine oligotrich ciliate, Omegastrombidium hongkongense n. sp., was isolated from a bloom of Noctiluca scuntillans near Port Shelter, Hong Kong. The morphology and infraciliature of this new species were studied on both living and protargol-stained specimens. Its phylogenetic position was discussed based on the sequence of the small subunit r RNA gene. O. hongkongense is different from its congeners with special characters. The cells are usually heart-shaped, and the cell size usually is(20–35) ×(20–30) μm in vivo. Its deep buccal cavity extends obliquely to about 1/2 of cell length. It shows prominent apical protrusion. The adoral zone of membranelles is divided into 17–19 collar membranelles and four buccal membranelles. It has one ball-like macronucleus. The girdle kinety forms a closed loop which obliquely surrounds the body. The ventral kinety and thigmotactic membranelles are not observed. The SSU r RNA sequence of O. hongkongense was close to those of Strombidium paracalkinsi and Varistrombidium kelum with approximately 99% similarity. In the phylogenetic trees, O. hongkongense can be grouped with O. elegans and V. kielum species with very low support(16% ML).展开更多
Prostomates and haptorians are two basal groups of ciliates with limited morphological characteristics available for taxonomy. Morphologically, the structures used to identify prostomates and haptorians are similar or...Prostomates and haptorians are two basal groups of ciliates with limited morphological characteristics available for taxonomy. Morphologically, the structures used to identify prostomates and haptorians are similar or even identical, which generate heavy taxonomic and phylogenetic confusion. In present work, phylogenetic positions lineage of two rare genera, Plagiopogon and Askenasia, were investigated. Three genes including small subunit ribosomal RNA gene(hereafter SSU r DNA), internal transcribed spacer region(ITS region), and large subunit ribosomal RNA gene(LSU r DNA) were analyzed, 10 new sequences five species each. Our findings included 1) class Prostomatea and order Haptorida are multiphyletic; 2) it may not be appropriate to place order Cyclotrichiida in subclass Haptoria, and the systematic lineage of order Cyclotrichiida needs to be verified further; 3) genus Plagiopogon branches consistently within a clade covering most prostomes and is basal of clade Colepidae, implying its close lineage to Prostomatea; and 4) Askenasia is phylogenetically distant from the subclass Haptoria but close to classes Prostomatea, Plagiopylea and Oligohymenophorea. We supposed that the toxicyst of Askenasia may be close to taxa of prostomes instead of haptorians, and the dorsal brush is a more typical morphological characteristics of haptorians than toxicysts.展开更多
In order to clarify the phylogeny and relationships of the most confused hypotrichous ciliates,Holosticha-complex,four closely related holostichids(five populations),Holosticha bradburyae,H.diademata,Anteholosticha ...In order to clarify the phylogeny and relationships of the most confused hypotrichous ciliates,Holosticha-complex,four closely related holostichids(five populations),Holosticha bradburyae,H.diademata,Anteholosticha sp.,and A.manca,were compared and analyzed using ITS2 secondary structures,ITS1-5.8S-ITS2 region and SSrRNA gene sequences.The ITS1-5.8S-ITS2 region sequences of these four species were first sequenced,and they shared sequence identities ranging from 68.0% to 90.1%,while two populations of Anteholosticha sp.differed in three nucleotides(sequence identity 99.8%).There were several minor differences among ITS2 secondary structures of these species,while two populations of Anteholosticha sp.had the identical secondary structure.Phylogenetic trees inferred from the ITS1-5.8S-ITS2 region sequences of stichotrichs using multiple algorithms(Neighbor-Joining,Maximum Parsimony and Bayesian) revealed similar topologies.The results show that:(1) Holosticha bradburyae and H.diademata firmly clustered together with strong bootstrap supports,forming a sister clade with Anteholosticha sp.,(2) Anteholosticha appeared to be a paraphyletic assemblage,in which the morphotype A.manca was more closely related to Diaxonella trimarginata than to its congener Anteholosticha sp.Phylogenetic analyses based on the SSrRNA gene and the combined sequences of SSrRNA gene and ITS1-5.8S-ITS2 region revealed the similar relationships between Holosticha and Anteholosticha,nevertheless their positions within the subclass Stichotrichia differed from each other inferred from different genes.展开更多
基金The National Natural Science Foundation of China under contract Nos 30570236,U0633006,40506033 and 40676076the Program for New Century Excellent Talents in Universities of China under contract No. NCET05-0595
文摘Microplankton communities of three coastal sites of Qingdao,Shandong Province,China were investigated using RAPD(random amplified polymorphic DNA) molecular markers and morphological observations.Eight RAPD-primers were selected to amplify the DNA polymorphy.The genetic distances inferred from the pairwise similarities were calculated for the phylogenetic tree construction.Meantime,the traditional microscopic determination,a way of visualizing the species composition,was performed to detect the major taxa of microplanktons from all samples.Results showed that:(1) the band sharing index values were in the range of 0.504 2-0.763 2 among samples from the same sampling site at different time scales,while 0.406 5-0.685 7 among the samples from different stations at the same time scales,indicating that spatial variations of microplankton communities were more pronounced than temporal ones;(2) samples from the same station basically clustered together,corresponding to the geographic distribution of the sampling sites;(3) diversity derived from genetic and morphological data did not correspond with each other well.
基金Supported by the National Natural Science Foundation of China(Nos.31772440,31430077,41576124,31761133001)the Pearl River Science and Technology Nova Program of Guangzhou(No.201610010162) to YZ+1 种基金Guangdong MEPP Fund(No.GDOE(2019)A23)the Special Support Program of Guangdong Province to YZ
文摘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.
基金supported by the National Natural Science Foundation of China(No.31301868)the Hong Kong Research Grants Council(Nos.GRF 661610 and 661912)+2 种基金the Hong Kong Scholar Programme(No.HKSP13SC03)NSFC-Guangdong Province Joint Foundation(No.U1301 235)Natural Science Foundation of Guangdong Pro-vince(No.S2013040013192)
文摘One new marine oligotrich ciliate, Omegastrombidium hongkongense n. sp., was isolated from a bloom of Noctiluca scuntillans near Port Shelter, Hong Kong. The morphology and infraciliature of this new species were studied on both living and protargol-stained specimens. Its phylogenetic position was discussed based on the sequence of the small subunit r RNA gene. O. hongkongense is different from its congeners with special characters. The cells are usually heart-shaped, and the cell size usually is(20–35) ×(20–30) μm in vivo. Its deep buccal cavity extends obliquely to about 1/2 of cell length. It shows prominent apical protrusion. The adoral zone of membranelles is divided into 17–19 collar membranelles and four buccal membranelles. It has one ball-like macronucleus. The girdle kinety forms a closed loop which obliquely surrounds the body. The ventral kinety and thigmotactic membranelles are not observed. The SSU r RNA sequence of O. hongkongense was close to those of Strombidium paracalkinsi and Varistrombidium kelum with approximately 99% similarity. In the phylogenetic trees, O. hongkongense can be grouped with O. elegans and V. kielum species with very low support(16% ML).
基金supported by the National Natural Science Foundation of China(Nos.31222050,41376141,3112041,and 31471973)the international research projects from King Saud University(Nos.RGP-VPP-083,IRG14-22)
文摘Prostomates and haptorians are two basal groups of ciliates with limited morphological characteristics available for taxonomy. Morphologically, the structures used to identify prostomates and haptorians are similar or even identical, which generate heavy taxonomic and phylogenetic confusion. In present work, phylogenetic positions lineage of two rare genera, Plagiopogon and Askenasia, were investigated. Three genes including small subunit ribosomal RNA gene(hereafter SSU r DNA), internal transcribed spacer region(ITS region), and large subunit ribosomal RNA gene(LSU r DNA) were analyzed, 10 new sequences five species each. Our findings included 1) class Prostomatea and order Haptorida are multiphyletic; 2) it may not be appropriate to place order Cyclotrichiida in subclass Haptoria, and the systematic lineage of order Cyclotrichiida needs to be verified further; 3) genus Plagiopogon branches consistently within a clade covering most prostomes and is basal of clade Colepidae, implying its close lineage to Prostomatea; and 4) Askenasia is phylogenetically distant from the subclass Haptoria but close to classes Prostomatea, Plagiopylea and Oligohymenophorea. We supposed that the toxicyst of Askenasia may be close to taxa of prostomes instead of haptorians, and the dorsal brush is a more typical morphological characteristics of haptorians than toxicysts.
基金The Natural Science Foundation of China under contract No. 30870264the Center of Excellence in Biodiversity,King Saud University,Saudi Arabia
文摘In order to clarify the phylogeny and relationships of the most confused hypotrichous ciliates,Holosticha-complex,four closely related holostichids(five populations),Holosticha bradburyae,H.diademata,Anteholosticha sp.,and A.manca,were compared and analyzed using ITS2 secondary structures,ITS1-5.8S-ITS2 region and SSrRNA gene sequences.The ITS1-5.8S-ITS2 region sequences of these four species were first sequenced,and they shared sequence identities ranging from 68.0% to 90.1%,while two populations of Anteholosticha sp.differed in three nucleotides(sequence identity 99.8%).There were several minor differences among ITS2 secondary structures of these species,while two populations of Anteholosticha sp.had the identical secondary structure.Phylogenetic trees inferred from the ITS1-5.8S-ITS2 region sequences of stichotrichs using multiple algorithms(Neighbor-Joining,Maximum Parsimony and Bayesian) revealed similar topologies.The results show that:(1) Holosticha bradburyae and H.diademata firmly clustered together with strong bootstrap supports,forming a sister clade with Anteholosticha sp.,(2) Anteholosticha appeared to be a paraphyletic assemblage,in which the morphotype A.manca was more closely related to Diaxonella trimarginata than to its congener Anteholosticha sp.Phylogenetic analyses based on the SSrRNA gene and the combined sequences of SSrRNA gene and ITS1-5.8S-ITS2 region revealed the similar relationships between Holosticha and Anteholosticha,nevertheless their positions within the subclass Stichotrichia differed from each other inferred from different genes.