Daming Li

Quantification of microcystin-producing and non-microcystin producing Microcystis populations during the 2009 and 2010 blooms in Lake Taihu using quantitative real-time PCR

Lake Taihu, a large, shallow hypertrophic freshwater lake in eastern China, has experienced lake-wide toxic cyanobacterial blooms annually during summer season in the past decades. Spatial changes in the abundance of hepatotoxin microcystin-producing and nonmicrocystin producing Microcystis populations were investigated in the lake in August of 2009 and 2010. To monitor the densities of the total Microcystis population and the potential microcystin-producing subpopulation, we used a quantitative real-time PCR assay targeting the phycocyanin intergenic spacer (PC-IGS) and the microcystin synthetase gene (mcyD), respectively. On the basis of quantification by real-time PCR analysis, the abundance of potential toxic Microcystis genotypes and the ratio of the mcyD subpopulation to the total Microcystis varied significantly, from 4.08 x 10(4) to 5.22 x 10(7) copies/mL, from 5.7% to 65.8%, respectively. Correlation analysis showed a strong positive relationship between chlorophyll-a, toxic Microcystis and total Microcystis; the abundance of toxic Microcystis correlated positively with total phosphorus and ortho-phosphate concentrations, but negatively with TN:TP ratio and nitrate concentrations. Meanwhile the proportion of potential toxic genotypes within Microcystis population showed positive correlation with total phosphorus and ortho-phosphate concentrations. Our data suggest that increased phosphorus loading may be a significant factor promoting the occurrence of toxic Microcystis bloom in Lake Taihu.

Temporal and spatial variation in fish assemblages in Lake Taihu, China

Set-net surveys were performed monthly between January 2010 and December 2012 at six sampling sites in Lake Taihu in order to determine the spatial and temporal variation in fish assemblages in Lake Taihu and to assess the influence on fish assemblages of eutrophication and disconnection of migration routes. A total of 134,604 specimens (1456.7 kg total biomass) were caught, representing 61 species, 18 families, and 10 orders. Cyprinidae fish (36 species) contributed most of the total species richness and the most dominant species was Coilia nasus. Sampling months and sampling sites each significantly affected the Margalef richness index, Shannon–Wiener diversity index (H′), and Piélous evenness index (J′) of fish assemblages and there were interactive effects between them. The ANOSIM analysis indicated that the fish assemblage structure had significant differences among the sample sites. Total nitrogen (TN) and total phosphorus (TP) both differed significantly among sites. The results of correlation analyses suggested that there was a significant negative correlation between two indices (H′ and J′) and both TP and TN (p < 0.01) as well as a significant positive correlation of catch per unit effort with both TP and TN (p < 0.01). Our results suggest that eutrophication in Lake Taihu has led to an increase in small-sized phytoplanktivorous and zooplanktivorous fishes and a decrease in prey availability for predatory fishes. Thus, the relative importance of small-sized fishes has increased and a few small-sized species (e.g., C. nasus) have become the dominant species, as reflected by reductions in the species diversity indices (H′ and J′).

Evaluation of genetic diversity and population structure of five yellow catfish Pelteobagrus fulvidraco populations by microsatellite markers

Abstract Yellow catfish, Pelteobagrus fulvidraco, is an important commercial freshwater species in China. Knowledge about the genetic diversity of the yellow catfish is important to support the management and conservation programs, which would subsequently support the sustainable production of this species. To investigate the genetic diversity and the structure of yellow catfish in the middle and lower reaches of the Yangtze River, 125 individuals from five lakes were genotyped using 13 microsatellite markers. Moderate genetic diversity was determined in all populations, with the observed heterozygosity (HO) ranging from 0.42 to 0.49 and the expected heterozygosity (HE) ranging from 0.51 to 0.61. Low to moderate genetic differentiation among the populations was revealed from pairwise FST values (p < 0.05), as well as from analysis of molecular variance (AMOVA). The UPGMA dendrogram and Bayesian clustering analysis indicated a correlation between genetic differences and geographic distance – four populations from the lower reaches clustered together, whereas the Poyang Lake (PY) population formed a separate cluster. The present study would be helpful in the wild stock management and artificial propagation programs for yellow catfish in the middle and lower reaches of the Yangtze River.

Dynamics of the bacterial community in a channel catfish nursery pond with a cage–pond integration system

The changes in the bacterial community composition in a channel catfish nursery pond with a cage-pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage-pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.

Complete mitochondrial genome of Odontobutis haifengensis (Perciformes, Odontobutiae): A unique rearrangement of tRNAs and additional non-coding regions identified in the genus Odontobutis

Herein, the complete mitochondrial genome of Odontobutis haifengensis was sequenced for the first time. The O. haifengensis mitogenome was 17,016bp in length and included 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The genome organization, base composition, codon usage, and gene rearrangement was similar to other Odontobutis species. Furthermore, a tRNA gene rearrangement within the SLH cluster was found to be identical to other Odontobutis species. Moreover, the gene order and the positions of additional intergenic non-coding regions suggests that the observed unique gene rearrangement resulted from a tandem duplication and random loss of large-scale gene regions. Additionally, phylogenetic analysis showed that Odontobutis species form a monophyletic clade due to the conserved mitochondrial gene rearrangement. This study provides useful information that aids in a better understanding of mitogenomic diversity and evolutionary patterns of Odontobutidae species.

Complete mitochondrial genome of Chinese icefish Neosalanx tangkahkeiis (Salmoniformes, Salangidae): comparison reveals Neosalanx taihuensis not a valid name

Abstract The complete mitochondrial genome of Neosalanx tangkahkeiis was determined to be 16,550 bp in length with (A+T) content of 49.7%, and it consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the N. tangkahkeiis complete mtDNA were identical to most of other vertebrates. The sequence comparison showed that mitogenome of N. tangkahkeiis had a 99.9% of similarity with so-called N. taihuensis, indicating they are the same species and N. taihuensis is not a valid name.