Yuanshao Lin

16S rRNA is a better choice than COI for DNA barcoding hydrozoans in the coastal waters of China

Identification of hydrozoan species is challenging, even for taxonomic experts, due to the scarcity of distinct morphological characters and phenotypic plasticity. DNA barcoding provides an efficient method for species identification, however, the choice between mitochondrial cytochrome c oxidase subunit I (COI) and large subunit ribosomal RNA gene (16S) as a standard barcode for hydrozoans is subject to debate. Herein, we directly compared the barcode potential of COI and 16S in hydrozoans using 339 sequences from 47 pelagic hydrozoan species. Analysis of Kimura 2-parameter genetic distances (K2P) documented the mean intraspecific/interspecific variation for COI and 16S to be 0.004/0.204 and 0.003/0.223, respectively. An obvious “barcoding gap” was detected for all species in both markers and all individuals of a species clustered together in both the COI and 16S trees. These results suggested that the species within the studied taxa can be efficiently and accurately identified by COI and 16S. Furthermore, our results confirmed that 16S was a better phylogenetic marker for hydrozoans at the genus level, and in some cases at the family level. Considering the resolution and effectiveness for barcoding and phylogenetic analyses of Hydrozoa, we strongly recommend 16S as the standard barcode for hydrozoans.

Phosphorus, Nitrogen and Chlorophyll-a Are Significant Factors Controlling Ciliate Communities in Summer in the Northern Beibu Gulf, South China Sea

Ciliates (protozoa) are ubiquitous components of plankton community and play important roles in aquatic ecosystems in regards of their abundance, biomass, diversity and energy turnover. Based on the stratified samples collected from the northern Beibu Gulf in August 2011, species composition, abundance, biomass, diversity and spatial pattern of planktonic ciliates were studied. Furthermore the main environmental factors controlling ciliate communities were determined. A total of 101 species belonging to 44 genera and 7 orders (i.e., Oligotrichida, Haptorida, Euplotida, Sessilida, Pleurostomatida, Scuticociliatida and Tintinnida) were identified. The variation of ciliate communities was significant at horizontal level, but that was not at vertical level. Based on cluster analysis, ciliate communities were divided into three main groups. Redundancy analysis (RDA) revealed that Group A, existing in the waters with higher concentration of phosphorus and nitrogen, was dominated by Tintinnidium primitivum. Group B in the waters with lower temperature and chlorophyll-a concentration, was dominated by Leegaardiella ovalis. Group C, existing in the waters with higher temperature and chlorophyll-a concentration, was dominated by large Strombidium spp. and Mesodinium rubrum. Combining multiple analytic methods, our results strongly supported that phosphorus, nitrogen and chlorophyll-a were the most significant factors affecting the ciliate communities in the northern Beibu Gulf in summer. Concentration of phosphorus and nitrogen primarily influenced ciliate biomass, implying a potential impact of eutrophication on ciliate growth. The correlation with chlorophyll-a concentration, on one hand indicate the response of ciliates to the food availability, and on the other hand, the ciliates containing chloroplasts or endosymbionts may contribute greatly to the chlorophyll-a.

Detection of a new Clytia species (Cnidaria: Hydrozoa: Campanulariidae) with DNA barcoding and life cycle analyses

National Natural Science Foundation of China [41006078]; Fundamental Research Funds for the Central Universities [2010121037]; Public Science and Technology Research Funds Projects of Ocean [201005015-5]; Natural Science Foundation of Fujian Province of China [2011J05116]

Spatial and seasonal variations of large tintinnid ciliates in Shenhu Bay of China

In this study, the spatial distribution and seasonal variation of large tintinnids (>76 μm) were investigated in Shenhu Bay during three seasons of 2012. Of the 36 species identified, 9 were dominant (i.e. Tintinnopsis radix, Leprotintinnus simplex, Tintinnopsis japonica, Tintinnopsis tubulosoides, Leprotintinnus nordqvisti, Tintinnopsis beroidea, Stenosemella parvicollis, Tintinnidium primitivum, Tintinnopsis nana). A clear seasonal shift of the taxonomic composition as well as the lorica size of the dominant species was observed. The highest numbers of tintinnid species occurred in spring, while the highest abundance and biomass occurred in summer. Clustering indicated that the seasonal variations of the community structure were more obvious than spatial variations. Spearman correlation analysis revealed that density of phytoplankton prey had a significant impact on the tintinnid abundance. Redundancy analysis (RDA) illustrated that temperature, salinity and the nutrient level were the most important abiotic factors affecting the spatial and seasonal pattern of tintinnid communities in Shenhu Bay.

Life Cycle Reversal in Aurelia sp.1 (Cnidaria, Scyphozoa).

The genus Aurelia is one of the major contributors to jellyfish blooms in coastal waters, possibly due in part to hydroclimatic and anthropogenic causes, as well as their highly adaptive reproductive traits. Despite the wide plasticity of cnidarian life cycles, especially those recognized in certain Hydroza species, the known modifications of Aurelia life history were mostly restricted to its polyp stage. In this study, we document the formation of polyps directly from the ectoderm of degenerating juvenile medusae, cell masses from medusa tissue fragments, and subumbrella of living medusae. This is the first evidence for back-transformation of sexually mature medusae into polyps in Aurelia sp.1. The resulting reconstruction of the schematic life cycle of Aurelia reveals the underestimated potential of life cycle reversal in scyphozoan medusae, with possible implications for biological and ecological studies.

Spatial pattern of the planktonic ciliate community and its relationship with the environment in spring in the northern Beibu Gulf, South China Sea

Surface water samples were collected from 19 sites in the northern Beibu Gulf in April 2011. Species composition and abundance of planktonic ciliates were investigated. They were combined with environmental data to obtain the spatial pattern of the ciliate community and its relationship with the environment. A total of 36 species belonging to 13 genera and 3 orders (Oligotrichida, Haptorida and Tintinnida) were identified, including 10 dominant species. All 19 samples were divided into three groups using cluster analysis and multidimensional scaling (MDS) on the basis of the ciliate species composition and abundance. Group 1 was the least abundant. The species of the order Oligotrichida dominated in Group 2. In contrast, Mesodinium species were of increased importance in Group 3. Redundancy analysis (RDA) revealed that ciliate communities were more closely related to the level of nitrogen (total nitrogen, nitrate nitrogen, nitrite nitrogen) and phosphorus (total phosphorus, active phosphorus) rather than other variables. As the levels of nitrogen and phosphorus increased, communities dominated by species from the order Oligotrichida were replaced by those dominated by Mesodinium species.

Morphology and molecular analyses of a new Clytia species (Cnidaria: Hydrozoa: Campanulariidae) from the East China Sea

The near-cosmopolitan genus Clytia is abundantly found in coastal waters, but difficulties of identification in this genus make nearly all species records of medusae suspect. Complex life histories, ambiguous taxonomic characters, and phenotypic plasticity pose serious problems for accurate species-level identifications and future revisions of Clytia species. In the present study, morphological investigations and molecular analyses of Clytia specimens from the coastal waters of the East China Sea revealed Clytia gulangensis sp. nov. as a new species. DNA barcoding based on the mitochondrial cytochrome oxidase I (COI) gene supported the new species as a separate species within Clytia , and phylogenetic analyses based on mitochondrial 16S rDNA and nuclear 18S rDNA further confirmed this new species to be a distinct lineage. Moreover, detailed observation of medusae and polyps of this species showed sufficient morphological differences from other Clytia species for a diagnosis. Our results indicated that life cycle and DNA-based studies should be a standard approach in future biodiversity investigations of Clytia species.

Genetic Diversity and Variance of Stentor coeruleus (Ciliophora: Heterotrichea) Inferred from Inter-Simple Sequence Repeat (ISSR) Fingerprinting

We used inter‐simple sequence repeat fingerprinting to analyze the genetic structure of 16 populations of Stentor coeruleus from three lakes and three ponds in China. Using 14 polymorphic primers, a total of 99 discernible DNA fragments were detected, among which 76 (76.77%) were polymorphic, indicating median genetic diversity in these populations. Further, both Neis gene diversity (h) and Shannons information index (I) between the different populations revealed a median genetic diversity. At the same time, gene flow was interpreted to be low. The main factors responsible for the median level of diversity and low gene flow within populations are probably due to a low frequency of sexual recombinations. Analysis of molecular variance showed that there was high genetic differentiation among the five water bodies. Both cluster analysis and a nonmetric multidimensional scaling analysis suggested that genotypes isolated from the same locations displayed a higher genetic similarity than those from different ones, separating populations into subgroups according to their geographical locations. However, there is a weak positive correlation between the genetic distance and geographical distance.

Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes

Unraveling the relative importance of ecological processes regulating microbial community structure is a central goal in microbial ecology. Here, we used high-throughput sequencing to examine the relative contribution of selective and neutral processes in the assembly of abundant and rare subcommunities from three subtropical bays of China. We found that abundant and rare bacterial taxa were distinctly different in diversity, despite the similar biogeographic patterns and strong distance-decay relationships, but the dispersal of rare bacterial taxa was more limited than that of abundant taxa. Furthermore, the environmental (selective processes) and spatial (neutral processes) factors seemed to govern the assembly and biogeography of abundant and rare bacterial subcommunities, although both factors explained only a small fraction of variation within the rare subcommunity. More importantly, variation partitioning (based on adjusted R2 in redundancy analysis) showed that spatial factors exhibited a slightly greater influence on both abundant and rare subcommunities compared to environmental selection; however, the abundant subcommunity had a much stronger response to spatial factors (17.3% of pure variance was explained) than that shown by the rare bacteria (3.5%). These results demonstrate that environmental selection and neutral processes explained the similar biogeographic patterns of abundant and rare subcommunities, but a large proportion of unexplained variation in the rare taxa (91.1%) implies that more complex assembly mechanisms may exist to shape the rare bacterial assemblages in the three subtropical bays.